Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 21
Found at i:841203 original size:28 final size:31
Alignment explanation
Indices: 841161--841223 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
841151 GGTCTTACAA
*
841161 TAAAACCCTAGAAA-TTGGGGAATTTTAAT-
1 TAAAACCCTAGAAATTTGGGAAATTTTAATC
841190 TAAAACCCTA-AAATTTGGGAAATTTTAATC
1 TAAAACCCTAGAAATTTGGGAAATTTTAATC
841220 TAAA
1 TAAA
841224 TTCATAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 3 0.10
29 24 0.77
30 4 0.13
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (31 bp):
TAAAACCCTAGAAATTTGGGAAATTTTAATC
Found at i:844111 original size:26 final size:26
Alignment explanation
Indices: 844075--844156 Score: 121
Period size: 26 Copynumber: 3.2 Consensus size: 26
844065 ATGGCACTAA
844075 GTGTA-TATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
*
844100 GTGTATTATGGTGGGCACGGCCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
* * *
844126 GTATATTATAGTGGGCAAGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
844152 GTGTA
1 GTGTA
844157 AGCACTATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
25 5 0.10
26 45 0.90
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.34
Consensus pattern (26 bp):
GTGTATTATGGTGGGCACGACCTTAT
Found at i:852931 original size:26 final size:26
Alignment explanation
Indices: 852895--852958 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
852885 ATGTAGACTT
852895 GAAGCGAAAAGAGATTGAATTTCAAG
1 GAAGCGAAAAGAGATTGAATTTCAAG
*
852921 GAAGCGAAAAGAGATTGAATTTGAAG
1 GAAGCGAAAAGAGATTGAATTTCAAG
*
852947 AAAGCGATAAAG
1 GAAGCGA-AAAG
852959 TTTTTCTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.28, T:0.17
Consensus pattern (26 bp):
GAAGCGAAAAGAGATTGAATTTCAAG
Found at i:854353 original size:30 final size:30
Alignment explanation
Indices: 854294--854362 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
854284 ACAAGCCTTA
* *
854294 GAAAAATT-GGGGACAATTTTATAATTTTT
1 GAAAAGTTGGGGGACAATTTGATAATTTTT
854323 GAAAAGTTGGGGGACTAATTTGATAA-TTTT
1 GAAAAGTTGGGGGAC-AATTTGATAATTTTT
854353 GTAAAAGTTG
1 G-AAAAGTTG
854363 TGAATGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.20
30 11 0.31
31 17 0.49
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
GAAAAGTTGGGGGACAATTTGATAATTTTT
Found at i:856220 original size:18 final size:18
Alignment explanation
Indices: 856193--856236 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
856183 ATGGGAATCA
*
856193 AAATACATTCTTCGGAAC
1 AAATATATTCTTCGGAAC
* **
856211 AAATATATTCTTTGGATT
1 AAATATATTCTTCGGAAC
856229 AAATATAT
1 AAATATAT
856237 GTTTCAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (18 bp):
AAATATATTCTTCGGAAC
Found at i:864557 original size:21 final size:21
Alignment explanation
Indices: 864528--864587 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
864518 ATTTACTGTG
864528 ATTGCGGCCGTCGCGGGTGCT
1 ATTGCGGCCGTCGCGGGTGCT
* **
864549 ATTGTGGCCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGTGCT
*
864570 ATTGCGGCCGTTGCGGGT
1 ATTGCGGCCGTCGCGGGT
864588 AACTCGGACA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.07, C:0.27, G:0.42, T:0.25
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGTGCT
Found at i:866770 original size:31 final size:31
Alignment explanation
Indices: 866733--866795 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
866723 GGAACTTATG
* *
866733 TTAAAATAAAATTATGCATAAACGTTTTGGC
1 TTAAAATAAAACTATGCAAAAACGTTTTGGC
*
866764 TTAAAATAGAACTATGCAAAAACGTTTTGGC
1 TTAAAATAAAACTATGCAAAAACGTTTTGGC
866795 T
1 T
866796 ACAAAGGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (31 bp):
TTAAAATAAAACTATGCAAAAACGTTTTGGC
Found at i:869227 original size:24 final size:27
Alignment explanation
Indices: 869200--869261 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
869190 GGATCTGCGC
869200 TGATCCAG-GA-AG-ATTTCTCGGTCA
1 TGATCCAGAGATAGAATTTCTCGGTCA
*
869224 TGAT-CAGAGATTCGAATTTCTCGGTCA
1 TGATCCAGAGA-TAGAATTTCTCGGTCA
869251 TGAT-CAGAGAT
1 TGATCCAGAGAT
869262 CCCGTGAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
26 2 0.06
27 22 0.67
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (27 bp):
TGATCCAGAGATAGAATTTCTCGGTCA
Found at i:869533 original size:20 final size:20
Alignment explanation
Indices: 869496--869536 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
869486 ATTCCACCTC
* *
869496 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
869516 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
869536 A
1 A
869537 AGGGCTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:876153 original size:219 final size:219
Alignment explanation
Indices: 875774--876211 Score: 876
Period size: 219 Copynumber: 2.0 Consensus size: 219
875764 AATCTAGCTC
875774 AAGAGTTCCATGTGTCTTACGCCCAAACCCATGCTTAGTTGAGGGAAACTGATAATCATTGGTAG
1 AAGAGTTCCATGTGTCTTACGCCCAAACCCATGCTTAGTTGAGGGAAACTGATAATCATTGGTAG
875839 CAATCCTATCCAAGATGTCAAATGCCTATGCCGGTGATTTATCTAGTAACGTCCCATTTGCCAAG
66 CAATCCTATCCAAGATGTCAAATGCCTATGCCGGTGATTTATCTAGTAACGTCCCATTTGCCAAG
875904 GCATCTAGCATCATCCTCGTGGGTGCGTTTACTCCATTATAGAACATCACTACTTGTGTCCAATC
131 GCATCTAGCATCATCCTCGTGGGTGCGTTTACTCCATTATAGAACATCACTACTTGTGTCCAATC
875969 TTGAAAACCATGGTTTGAACACTT
196 TTGAAAACCATGGTTTGAACACTT
875993 AAGAGTTCCATGTGTCTTACGCCCAAACCCATGCTTAGTTGAGGGAAACTGATAATCATTGGTAG
1 AAGAGTTCCATGTGTCTTACGCCCAAACCCATGCTTAGTTGAGGGAAACTGATAATCATTGGTAG
876058 CAATCCTATCCAAGATGTCAAATGCCTATGCCGGTGATTTATCTAGTAACGTCCCATTTGCCAAG
66 CAATCCTATCCAAGATGTCAAATGCCTATGCCGGTGATTTATCTAGTAACGTCCCATTTGCCAAG
876123 GCATCTAGCATCATCCTCGTGGGTGCGTTTACTCCATTATAGAACATCACTACTTGTGTCCAATC
131 GCATCTAGCATCATCCTCGTGGGTGCGTTTACTCCATTATAGAACATCACTACTTGTGTCCAATC
876188 TTGAAAACCATGGTTTGAACACTT
196 TTGAAAACCATGGTTTGAACACTT
876212 GCGAAGCAAT
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 219 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (219 bp):
AAGAGTTCCATGTGTCTTACGCCCAAACCCATGCTTAGTTGAGGGAAACTGATAATCATTGGTAG
CAATCCTATCCAAGATGTCAAATGCCTATGCCGGTGATTTATCTAGTAACGTCCCATTTGCCAAG
GCATCTAGCATCATCCTCGTGGGTGCGTTTACTCCATTATAGAACATCACTACTTGTGTCCAATC
TTGAAAACCATGGTTTGAACACTT
Found at i:878439 original size:26 final size:27
Alignment explanation
Indices: 878408--878458 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
878398 ATCCAGGCAG
878408 ATTTCTCGGTC-TGATCAGAGATCCAA
1 ATTTCTCGGTCATGATCAGAGATCCAA
878434 ATTTCTCGGTCATGATCAGAGATCC
1 ATTTCTCGGTCATGATCAGAGATCC
878459 CGTGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAGAGATCCAA
Found at i:878728 original size:20 final size:20
Alignment explanation
Indices: 878691--878732 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
878681 ATTCTACCTC
* *
878691 ATGCAACTACATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
878711 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
878731 AT
1 AT
878733 AGGCTATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:887907 original size:29 final size:30
Alignment explanation
Indices: 887868--887940 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
887858 TTGTATTGTT
*
887868 TATACCACTAAACTTTTAATTTTG-TCAAC
1 TATACCACTAAACTTTGAATTTTGTTCAAC
* * *
887897 TATAGCACTAAACTTTGATTTTTGTTTCAAT
1 TATACCACTAAACTTTGAATTTTG-TTCAAC
887928 TATACCACTAAAC
1 TATACCACTAAAC
887941 CATTAAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.41
Consensus pattern (30 bp):
TATACCACTAAACTTTGAATTTTGTTCAAC
Found at i:889268 original size:2 final size:2
Alignment explanation
Indices: 889261--889299 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
889251 ATTAACTTCT
889261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
889300 GTGCTTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:889871 original size:269 final size:268
Alignment explanation
Indices: 889392--889932 Score: 750
Period size: 269 Copynumber: 2.0 Consensus size: 268
889382 AACCAGATGA
* *
889392 TGACACATGTCACCATCTGGTTGGATGATAAATAATTAAATTATAATTAAAGAAATTATCATTTA
1 TGACACATGTCACCATCTGGTTGGAAGATAAATAATTAAATTAAAATTAAAGAAATTATCATTTA
* *
889457 ATCTAATGATGACATGTGTAACCATCTAATTGGATTGATACTTTATTGAATAAAATTAAAATTAG
66 ATCTAATGATGACATGTGTAACCATCTAATTGGATGGATAATTTATTGAATAAAATTAAAATTAG
* *
889522 GACCAAATTGGTTGAATGTAAAGTATTGAGGTTCAAATATATAATTATACCAATTTTTTAACTAC
131 GACCAAATTGATTGAATGTAAAGTATTGAGGATCAAATATATAATTATACCAATTTTTTAACTAC
* * * **
889587 CACATAAGCACTTCTGTTCAATAATAACGTCT-GGTGGCTATATTGAACCCAATTAAATAATTTT
196 CACATAAACACTTCTGTTAAATAATAACGT-TGGGT-GCTATATTGAACACAATTAAATAATTCA
889651 GTAGTCATAT
259 GTAGTCATAT
*
889661 TGACACAATGTCACCATTTGGTT-GAAGATAAATAATTAAATTAAAATTAAAGAAATTATCATTT
1 TGACAC-ATGTCACCATCTGGTTGGAAGATAAATAATTAAATTAAAATTAAAGAAATTATCATTT
* * * * *
889725 AATCTAAT-ATTGACATGTGTCATCGTCTGATTGGATGGATAATTTATT-AGTTAAAATTAAAAT
65 AATCTAATGA-TGACATGTGTAACCATCTAATTGGATGGATAATTTATTGA-ATAAAATTAAAAT
* * * *
889788 TA-GACCAATTTGATTGGATGTACAAGTATTGTGGATCAAATATGTAATTATACCAATTTTTTAA
128 TAGGACCAAATTGATTGAATGTA-AAGTATTGAGGATCAAATATATAATTATACCAATTTTTTAA
** * * * *
889852 CTGTCACATAAACACTTCTGTTAAATACTAATGTTGGGTGCTATATTGGACATAATTAAATAATT
192 CTACCACATAAACACTTCTGTTAAATAATAACGTTGGGTGCTATATTGAACACAATTAAATAATT
889917 CAGTAGTCATAT
257 CAGTAGTCATAT
889929 TGAC
1 TGAC
889933 GTAATTTTAA
Statistics
Matches: 240, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
268 57 0.24
269 168 0.70
270 15 0.06
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (268 bp):
TGACACATGTCACCATCTGGTTGGAAGATAAATAATTAAATTAAAATTAAAGAAATTATCATTTA
ATCTAATGATGACATGTGTAACCATCTAATTGGATGGATAATTTATTGAATAAAATTAAAATTAG
GACCAAATTGATTGAATGTAAAGTATTGAGGATCAAATATATAATTATACCAATTTTTTAACTAC
CACATAAACACTTCTGTTAAATAATAACGTTGGGTGCTATATTGAACACAATTAAATAATTCAGT
AGTCATAT
Found at i:893862 original size:54 final size:54
Alignment explanation
Indices: 893803--894026 Score: 385
Period size: 54 Copynumber: 4.1 Consensus size: 54
893793 GTCAACATAG
* *
893803 ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGCGGCCTGAATTGTTTA
1 ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGGGGCCTGAATTGTTCA
*
893857 ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGAGGCCTGAATTGTTCA
1 ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGGGGCCTGAATTGTTCA
* *
893911 ACTGCTGGAGAAGTGAATTAGACGCATTTGGCATATTGGGGCCTGACTTGTTCA
1 ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGGGGCCTGAATTGTTCA
* *
893965 ACTGCTGGAGAAGTGAGTTAGATGCATTTGGCATATTGGGGCTTGAATTGTTCA
1 ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGGGGCCTGAATTGTTCA
894019 ACTGCTGG
1 ACTGCTGG
894027 GGACTGTATA
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 161 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (54 bp):
ACTGCTGGAGAAGTGAATTAGATGCATTTGGCATATTGGGGCCTGAATTGTTCA
Found at i:895350 original size:192 final size:192
Alignment explanation
Indices: 894770--896012 Score: 1311
Period size: 192 Copynumber: 6.5 Consensus size: 192
894760 TTGTTGCGAC
** * * * * *
894770 TGAAATGGTTGAGTCGAATAACTTCCATTTTGTGGGAG-TGTTTCCGTCT-ACTCAAGATGAGAG
1 TGAAATGGTTGAGTCTTATAACCTCTATTTTGTGAGAGAT-TTTCCGTCTGA-TCAAGATTATAG
* * * * * *
894833 ATACATTAACTAAGAACTATATAATGTAGTGTAAATAGATTATAACACATTGACATAGAATTAGA
64 ATAAATTAACTAAGAATTATATAATGTATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGA
*
894898 GGTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAA-CTGAGTTAACCACATGCTCCGAG
129 GGTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATC-GAGTTAACCACATGCTCTGAG
** * ** * *
894962 TGAAATGACTGAGTCGTATAATTTTTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATATAT
1 TGAAATGGTTGAGTCTTATAACCTCTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGAT
* * *
895027 AAATTAAATAAGGATTATATAATGTAGTTGTTAATAGGTTATAACTCATTGGCATAGAATTAGAG
66 AAATTAACTAAGAATTATATAATGTA-TTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAG
* * * * * *
895092 GTTACCGGTCCAATATCACCGTTGACCTGGCTTGTTTGAATTGAGTTAACCACATGCTCCGAG
130 GTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAG
* ** *
895155 TGAAATGGCTGAGTCTTATAACCTCTATTTTGTGAGAGATTTTCTATCTGATCAATATTATAGAT
1 TGAAATGGTTGAGTCTTATAACCTCTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGAT
* * *
895220 AAATTAAATAAGAATCATATAATATATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAGG
66 AAATTAACTAAGAATTATATAATGTATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAGG
* * *
895285 TTACCAATCCAGTATCACCGTTGACCTGGTTTATTTGAATCGAGTTAACCACATGCTCTGAG
131 TTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAG
* * * ** *
895347 TGAAATGGTTGAGTCGTATAACCTCTATTTTGTGAGATATTTCCCGTCTGATCGTGATTATAGCT
1 TGAAATGGTTGAGTCTTATAACCTCTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGAT
* * * *
895412 AAATTAACTAAGGATTACATAATGTAGTT-TAAATAGTTTATAACTCATTGTCATAGAATTAGAG
66 AAATTAACTAAGAATTATATAATGTA-TTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAG
* * * * * * *
895476 GTTACCAATCCAGTATCACCGTTGACCTGATTTTTTTGAATTGAGCTAAACACATGCTCTGAG
130 GTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAG
* * * * *
895539 TGAAATGGTTGAGTCGTCGTATAATCTCTATTTTTTGAGAGATTTTTCATCTGATCAACATTATA
1 TGAAATGGTTGAGTC-T--TATAACCTCTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATA
* * * * * * ** *
895604 GATAAATTAATTAAGAATTATATAATCTAATATAAAGAAGTTATAACTCATTGGCATTTAATTAT
63 GATAAATTAACTAAGAATTATATAATGTATTGTAAATAGGTTATAACTCATTGGCATAGAATTAG
* * * *
895669 TGGTTACCAGTTCAGTATCACCATTGACTTGGTTTGTTTGAATCGAGTTAATCACATGCTCTGAG
128 AGGTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAG
* * * * *
895734 TGAAATGGTTGAGT-TGTATAACTTTTATTTTGTGAAAGATTTTCCGCCT-ATTCAAGATAATAG
1 TGAAATGGTTGAGTCT-TATAACCTCTATTTTGTGAGAGATTTTCCGTCTGA-TCAAGATTATAG
* * * * * * * * * * * *
895797 ATAAATTAACTAAAAATTATATAATTTAGTGCAAATAAGTTATAATTGATCGACATATAGTGAGA
64 ATAAATTAACTAAGAATTATATAATGTATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGA
* * * * * * *
895862 GGTTACCATTCCAAT-TCGACCATTGACTTGATTTGTTTGAA-CTAAGTTGACCCCATGCTCTGA
129 GGTTACCAGTCCAGTATC-ACCATTGACCTGGTTTGTTTGAATC-GAGTTAACCACATGCTCTGA
895925 G
192 G
* * * * * * * *
895926 TGTAATGGTTGAGTC-GAGTAACCTCTATTTTGTGGGAGCTCTTT-TGTCTGATAAAGATGAGAG
1 TGAAATGGTTGAGTCTTA-TAACCTCTATTTTGTGAGAGAT-TTTCCGTCTGATCAAGATTATAG
*
895989 ATAAATTAAC-AAGAACTATATAAT
64 ATAAATTAACTAAGAATTATATAAT
896013 AAAACGTAAA
Statistics
Matches: 888, Mismatches: 147, Indels: 33
0.83 0.14 0.03
Matches are distributed among these distances:
191 17 0.02
192 536 0.60
193 178 0.20
194 1 0.00
195 156 0.18
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (192 bp):
TGAAATGGTTGAGTCTTATAACCTCTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGAT
AAATTAACTAAGAATTATATAATGTATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAGG
TTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAG
Found at i:895711 original size:387 final size:383
Alignment explanation
Indices: 894770--896031 Score: 1396
Period size: 387 Copynumber: 3.3 Consensus size: 383
894760 TTGTTGCGAC
* * * * ** * * *
894770 TGAAATGGTTGAGTCG-AATAACTTCCATTTTGTGGGAG-TGTTTCCGTCT-ACTCAAGATGAGA
1 TGAAATGGTTGAGTCGTTATAACCTCTATTTTGTGAGAGAT-TTTCTATCTGA-TCAACATTATA
* * * * * * * *
894832 GATACATTAACTAAGAACTATATAATGTAGTGTAAATAGATTATAACACATTGACATAGAATTAG
64 GATAAATTAAATAAGAATTATATAATATAATGTAAAAAG-TTATAACTCATTGGCATAGAATTAG
*
894897 AGGTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAA-CTGAGTTAACCACATGCTCCGA
128 AGGTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATC-GAGTTAACCACATGCTCTGA
** * *
894961 GTGAAATGACTGAGTCGTATAATTTTTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATATA
192 GTGAAATGGTTGAGTCGTATAACTTTTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGA
* * *
895026 TAAATTAAATAAGGATTATATAATGTAGTTGTTAATAGGTTATAACTCATTGGCATAGAATTAGA
257 TAAATTAACTAAGGATTATATAATGTAGTT-TAAATA-GTTATAACTCATTGACATAGAATTAGA
** ** *
895091 GGTTACCGGTCCAATATCACCGTTGACCTGGCTTGTTTGAATTGAGTTAACCACATGCTCCGAG
320 GGTTACCAATCCAATATCACCGTTGACCTGATTTGTTTGAATTGAGTTAACCACATGCTCTGAG
* *
895155 TGAAATGGCTGAGTC-TTATAACCTCTATTTTGTGAGAGATTTTCTATCTGATCAATATTATAGA
1 TGAAATGGTTGAGTCGTTATAACCTCTATTTTGTGAGAGATTTTCTATCTGATCAACATTATAGA
* * *
895219 TAAATTAAATAAGAATCATATAATATATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAG
66 TAAATTAAATAAGAATTATATAATATAATGTAAA-AAGTTATAACTCATTGGCATAGAATTAGAG
* * *
895284 GTTACCAATCCAGTATCACCGTTGACCTGGTTTATTTGAATCGAGTTAACCACATGCTCTGAGTG
130 GTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAGTG
* * * * ** *
895349 AAATGGTTGAGTCGTATAACCTCTATTTTGTGAGATATTTCCCGTCTGATCGTGATTATAGCTAA
195 AAATGGTTGAGTCGTATAACTTTTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGATAA
* *
895414 ATTAACTAAGGATTACATAATGTAGTTTAAATAGTTTATAACTCATTGTCATAGAATTAGAGGTT
260 ATTAACTAAGGATTATATAATGTAGTTTAAATAG-TTATAACTCATTGACATAGAATTAGAGGTT
* * * *
895479 ACCAATCCAGTATCACCGTTGACCTGATTTTTTTGAATTGAGCTAAACACATGCTCTGAG
324 ACCAATCCAATATCACCGTTGACCTGATTTGTTTGAATTGAGTTAACCACATGCTCTGAG
* *
895539 TGAAATGGTTGAGTCGTCGTATAATCTCTATTTTTTGAGAGATTTT-TCATCTGATCAACATTAT
1 TGAAATGGTTGAGTCGT--TATAACCTCTATTTTGTGAGAGATTTTCT-ATCTGATCAACATTAT
* * * **
895603 AGATAAATTAATTAAGAATTATATAATCTAATATAAAGAAGTTATAACTCATTGGCATTTAATTA
63 AGATAAATTAAATAAGAATTATATAATATAATGTAAA-AAGTTATAACTCATTGGCATAGAATTA
** * * *
895668 TTGGTTACCAGTTCAGTATCACCATTGACTTGGTTTGTTTGAATCGAGTTAATCACATGCTCTGA
127 GAGGTTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGA
* * * *
895733 GTGAAATGGTTGAGTTGTATAACTTTTATTTTGTGAAAGATTTTCCGCCT-ATTCAAGATAATAG
192 GTGAAATGGTTGAGTCGTATAACTTTTATTTTGTGAGAGATTTTCCGTCTGA-TCAAGATTATAG
** * ** * * * * * *
895797 ATAAATTAACTAAAAATTATATAATTTAGTGCAAATAAGTTATAATTGATCGACATATAGTGAGA
256 ATAAATTAACTAAGGATTATATAATGTAGTTTAAAT-AGTTATAACTCATTGACATAGAATTAGA
* * * * * * *
895862 GGTTACCATTCCAAT-TCGACCATTGACTTGATTTGTTTGAACTAAGTTGACCCCATGCTCTGAG
320 GGTTACCAATCCAATATC-ACCGTTGACCTGATTTGTTTGAATTGAGTTAACCACATGCTCTGAG
* * * * * * * *
895926 TGTAATGGTTGAGTCG--AGTAACCTCTATTTTGTGGGAGCTCTTT-TGTCTGATAAAGATGAGA
1 TGAAATGGTTGAGTCGTTA-TAACCTCTATTTTGTGAGAGAT-TTTCTATCTGATCAACATTATA
* * * * *
895988 GATAAATT-AACAAGAACTATATAATAAAACGTAAATGAGTTATA
64 GATAAATTAAATAAGAATTATATAATATAATGTAAA-AAGTTATA
896032 TATGATGGGT
Statistics
Matches: 739, Mismatches: 123, Indels: 32
0.83 0.14 0.04
Matches are distributed among these distances:
383 29 0.04
384 137 0.19
385 245 0.33
386 8 0.01
387 318 0.43
388 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (383 bp):
TGAAATGGTTGAGTCGTTATAACCTCTATTTTGTGAGAGATTTTCTATCTGATCAACATTATAGA
TAAATTAAATAAGAATTATATAATATAATGTAAAAAGTTATAACTCATTGGCATAGAATTAGAGG
TTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAATCGAGTTAACCACATGCTCTGAGTGA
AATGGTTGAGTCGTATAACTTTTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATAGATAAA
TTAACTAAGGATTATATAATGTAGTTTAAATAGTTATAACTCATTGACATAGAATTAGAGGTTAC
CAATCCAATATCACCGTTGACCTGATTTGTTTGAATTGAGTTAACCACATGCTCTGAG
Found at i:895869 original size:579 final size:576
Alignment explanation
Indices: 894770--896012 Score: 1453
Period size: 579 Copynumber: 2.2 Consensus size: 576
894760 TTGTTGCGAC
* * * *
894770 TGAAATGGTTGAGTCGAATAACTTCCATTTTGTGGGAGTGTTTCCGTCTACTCAAGATGAGAGAT
1 TGAAATGGTTGAGTCG-ATAACCTCTATTTTGTGAGAGTATTTCCGTCTACTCAAGATGAGAGAT
* *
894835 ACATTAACTAAGAACTATATAATGTAGTGTAAATAGATTATAACACATTGACATAGAATTAGAGG
65 AAATTAACTAAGAACTACATAATGTAGTGTAAATAGATTATAACACATTGACATAGAATTAGAGG
* * * *
894900 TTACCAGTCCAGTATCACCATTGACCTGGTTTGTTTGAACTGAGTTAACCACATGCTCCGAGTGA
130 TTACCAATCCAGTATCACCATTGACCTGATTTGTTTGAACTGAGCTAAACACATGCTCCGAGTGA
* * * * *
894965 AATGACTGAGTCGTATAATTTTTATTTTGTGAGAGATTTTCCGTCTGATCAAGATTATATATAAA
195 AATGACTGAGTCGTATAATCTCTATTTTGTGAGAGATTTTCCATCTGATCAACATTATAGATAAA
* * * * * * *
895030 TTAAATAAGGATTATATAATGTAGTTGTTAATAGGTTATAACTCATTGGCATAGAATTAGAGGTT
260 TTAAATAAGAATTATATAATCTAGATATAAAGAAGTTATAACTCATTGGCATAGAATTAGAGGTT
* * *
895095 ACCGGTCCAATATCACCGTTGACCTGGCTTGTTTGAATTGAGTTAACCACATGCTCCGAGTGAAA
325 ACCAGTCCAATATCACCATTGACCTGGCTTGTTTGAATCGAGTTAACCACATGCTCCGAGTGAAA
* * * * *
895160 TGGCTGAGTCTTATAACCTCTATTTTGTGAGAGATTTTCTATCTGATCAATATTATAGATAAATT
390 TGGCTGAGTCTTATAACCTCTATTTTGTGAAAGATTTTCCACCTGATCAAGATAATAGATAAATT
* * * * * * *
895225 AAATAAGAATCATATAATATATTGTAAATAGGTTATAACTCATTGGCATAGAATTAGAGGTTACC
455 AAATAAAAATCATATAATATAGTGCAAATAAGTTATAACTCATCGACATAGAATGAGAGGTTACC
* * * *
895290 AATCCAGTATC-ACCGTTGACCTGGTTTATTTGAA-TCGAGTTAACCACATGCTCTGAG
520 AATCCAAT-TCGACCATTGACCTGATTTATTTGAACT-AAGTTAACCACATGCTCTGAG
** * *
895347 TGAAATGGTTGAGTCGTATAACCTCTATTTTGTGAGA-TATTTCCCGTCTGA-TCGTGATTATAG
1 TGAAATGGTTGAGTCG-ATAACCTCTATTTTGTGAGAGTATTT-CCGTCT-ACTCAAGATGAGAG
* * * * * * *
895410 CTAAATTAACTAAGGATTACATAATGTAGTTTAAATAGTTTATAACTCATTGTCATAGAATTAGA
63 ATAAATTAACTAAGAACTACATAATGTAGTGTAAATAGATTATAACACATTGACATAGAATTAGA
* * * *
895475 GGTTACCAATCCAGTATCACCGTTGACCTGATTTTTTTGAATTGAGCTAAACACATGCTCTGAGT
128 GGTTACCAATCCAGTATCACCATTGACCTGATTTGTTTGAACTGAGCTAAACACATGCTCCGAGT
** * *
895540 GAAATGGTTGAGTCGTCGTATAATCTCTATTTTTTGAGAGATTTTTCATCTGATCAACATTATAG
193 GAAATGACTGA---GTCGTATAATCTCTATTTTGTGAGAGATTTTCCATCTGATCAACATTATAG
* ** *
895605 ATAAATTAATTAAGAATTATATAATCTA-ATATAAAGAAGTTATAACTCATTGGCATTTAATTAT
255 ATAAATTAAATAAGAATTATATAATCTAGATATAAAGAAGTTATAACTCATTGGCATAGAATTAG
* * * * * * *
895669 TGGTTACCAGTTCAGTATCACCATTGACTTGGTTTGTTTGAATCGAGTTAATCACATGCTCTGAG
320 AGGTTACCAGTCCAATATCACCATTGACCTGGCTTGTTTGAATCGAGTTAACCACATGCTCCGAG
* * * *
895734 TGAAATGGTTGAGT-TGTATAACTTTTATTTTGTGAAAGATTTTCCGCCT-ATTCAAGATAATAG
385 TGAAATGGCTGAGTCT-TATAACCTCTATTTTGTGAAAGATTTTCCACCTGA-TCAAGATAATAG
* * * * * * *
895797 ATAAATTAACTAAAAATTATATAATTTAGTGCAAATAAGTTATAATTGATCGACATATAGTGAGA
448 ATAAATTAAATAAAAATCATATAATATAGTGCAAATAAGTTATAACTCATCGACATAGAATGAGA
* * * * *
895862 GGTTACCATTCCAATTCGACCATTGACTTGATTTGTTTGAACTAAGTTGACCCCATGCTCTGAG
513 GGTTACCAATCCAATTCGACCATTGACCTGATTTATTTGAACTAAGTTAACCACATGCTCTGAG
* * * * *
895926 TGTAATGGTTGAGTCGAGTAACCTCTATTTTGTGGGAGCTCTTT-TGTCTGA-TAAAGATGAGAG
1 TGAAATGGTTGAGTCGA-TAACCTCTATTTTGTGAGAG-TATTTCCGTCT-ACTCAAGATGAGAG
*
895989 ATAAATTAAC-AAGAACTATATAAT
63 ATAAATTAACTAAGAACTACATAAT
896013 AAAACGTAAA
Statistics
Matches: 553, Mismatches: 101, Indels: 23
0.82 0.15 0.03
Matches are distributed among these distances:
576 4 0.01
577 169 0.31
578 17 0.03
579 289 0.52
580 70 0.13
581 4 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (576 bp):
TGAAATGGTTGAGTCGATAACCTCTATTTTGTGAGAGTATTTCCGTCTACTCAAGATGAGAGATA
AATTAACTAAGAACTACATAATGTAGTGTAAATAGATTATAACACATTGACATAGAATTAGAGGT
TACCAATCCAGTATCACCATTGACCTGATTTGTTTGAACTGAGCTAAACACATGCTCCGAGTGAA
ATGACTGAGTCGTATAATCTCTATTTTGTGAGAGATTTTCCATCTGATCAACATTATAGATAAAT
TAAATAAGAATTATATAATCTAGATATAAAGAAGTTATAACTCATTGGCATAGAATTAGAGGTTA
CCAGTCCAATATCACCATTGACCTGGCTTGTTTGAATCGAGTTAACCACATGCTCCGAGTGAAAT
GGCTGAGTCTTATAACCTCTATTTTGTGAAAGATTTTCCACCTGATCAAGATAATAGATAAATTA
AATAAAAATCATATAATATAGTGCAAATAAGTTATAACTCATCGACATAGAATGAGAGGTTACCA
ATCCAATTCGACCATTGACCTGATTTATTTGAACTAAGTTAACCACATGCTCTGAG
Found at i:915838 original size:20 final size:21
Alignment explanation
Indices: 915815--915883 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
915805 GTCGTTGGCC
*
915815 GTTGACTTTCACTTTTG-TTT
1 GTTGACTTTCACTTTTGACTT
* *
915835 GTTGATTTTGAC-TTTGACTT
1 GTTGACTTTCACTTTTGACTT
*
915855 -TTGACCTTTCACTTTTGACCT
1 GTTGA-CTTTCACTTTTGACTT
915876 -TTGACTTT
1 GTTGACTTT
915884 GAACATCTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 8 0.20
20 21 0.52
21 11 0.28
ACGTcount: A:0.13, C:0.17, G:0.14, T:0.55
Consensus pattern (21 bp):
GTTGACTTTCACTTTTGACTT
Found at i:915859 original size:7 final size:7
Alignment explanation
Indices: 915836--915883 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
915826 CTTTTGTTTG
915836 TTGA-TT
1 TTGACTT
915842 TTGAC-T
1 TTGACTT
915848 TTGACTT
1 TTGACTT
*
915855 TTGACCT
1 TTGACTT
*
915862 TTCACTT
1 TTGACTT
*
915869 TTGACCT
1 TTGACTT
915876 TTGACTT
1 TTGACTT
915883 T
1 T
915884 GAACATCTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (7 bp):
TTGACTT
Found at i:915868 original size:14 final size:14
Alignment explanation
Indices: 915836--915883 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
915826 CTTTTGTTTG
915836 TTGA-TTTTGA-CT
1 TTGACTTTTGACCT
915848 TTGACTTTTGACCT
1 TTGACTTTTGACCT
*
915862 TTCACTTTTGACCT
1 TTGACTTTTGACCT
915876 TTGACTTT
1 TTGACTTT
915884 GAACATCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 4 0.12
13 6 0.19
14 22 0.69
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (14 bp):
TTGACTTTTGACCT
Found at i:922352 original size:64 final size:63
Alignment explanation
Indices: 922284--922503 Score: 232
Period size: 64 Copynumber: 3.5 Consensus size: 63
922274 TTGAAGGTGT
** ** *
922284 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAAATAAATACATCGAATGCAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAAAATAAA-ACATCGAATGCAATTAGTGC
** *
922348 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGATTGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAA-AATAAAACATCGAATGCAATTAGTGC
* * * *
922412 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAA-ACAACATCGAATACATTTTA-TG
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAA-AATAAAACATCGAATGCA-ATTAGTG
922474 C
63 C
* *
922475 ACCGATGCATTAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
922504 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.01
63 37 0.28
64 88 0.66
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAAAATAAAACATCGAATGCAATTAGTGC
Found at i:923446 original size:103 final size:103
Alignment explanation
Indices: 923222--923439 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
923212 GTCGAGGGTC
* *
923222 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
923287 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
923325 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
*
923390 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
923428 TATGTGGTCCTT
1 TATGTGGTCCTT
923440 ATGGACAGTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:923482 original size:23 final size:23
Alignment explanation
Indices: 923449--923523 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
923439 TATGGACAGT
923449 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
923470 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* **
923493 ATTATATGTGGCACTTTGGTGCA
1 ATTATATGCGGCACTACGGTGCA
923516 ATTATATG
1 ATTATATG
923524 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.13
23 40 0.87
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:928319 original size:63 final size:62
Alignment explanation
Indices: 928186--928404 Score: 228
Period size: 63 Copynumber: 3.5 Consensus size: 62
928176 TTGAAGGTGT
** ** * *
928186 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAAATAAATACATCGAATGCAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATT--AATAAAAACATCGAATGCAATTAGTGC
*
928250 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATA-AAAACATCGAATGCAATTAGTGC
* * * * *
928313 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAACATCAAATACATTTTA-TGC
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAAA-AACATCGAATGCA-ATTAGTGC
* *
928376 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
928405 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
62 7 0.05
63 91 0.68
64 34 0.26
65 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAAAACATCGAATGCAATTAGTGC
Found at i:929410 original size:103 final size:102
Alignment explanation
Indices: 929122--929438 Score: 550
Period size: 103 Copynumber: 3.1 Consensus size: 102
929112 GTCGAGGGTC
929122 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
929187 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
65 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
929225 TATGTGGTCC-T--GACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
929287 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
929324 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
929389 TTGATCCATAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
929427 TATGTGGTCCTT
1 TATGTGGTCCTT
929439 ATGGACAGTA
Statistics
Matches: 205, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
99 97 0.47
100 1 0.00
102 1 0.00
103 106 0.52
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:929506 original size:23 final size:23
Alignment explanation
Indices: 929454--929522 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
929444 CAGTATTATA
*
929454 TGGCACTAC-GGTGCAATTCTATG
1 TGGCACT-CTGGTGCAATTATATG
* *
929477 CGACACTCTGGTGCAATTATATG
1 TGGCACTCTGGTGCAATTATATG
* *
929500 TGGCACTTTGGTGTAATTATATG
1 TGGCACTCTGGTGCAATTATATG
929523 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGCACTCTGGTGCAATTATATG
Found at i:933165 original size:3 final size:3
Alignment explanation
Indices: 933143--933205 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
933133 TGTTTCTTTA
*
933143 AAT AAA AAT -AT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
933189 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
933206 CGTTCATTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:935992 original size:2 final size:2
Alignment explanation
Indices: 935972--936018 Score: 53
Period size: 2 Copynumber: 23.5 Consensus size: 2
935962 TGCTTATTTC
935972 AT AT ACT AT A- AT CAT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
936014 CT AT A
1 AT AT A
936019 GCTATTATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 2 0.05
2 33 0.85
3 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:943110 original size:53 final size:53
Alignment explanation
Indices: 943011--943372 Score: 371
Period size: 53 Copynumber: 6.9 Consensus size: 53
943001 TCTTCGAACG
* * ***
943011 ACGGGTCCGCTCCCTCTTG-TTCAGGGA-TAAAGGAACTCGAACAATCTTCTAAAA
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGT--A-GAACTCGAACAATCTTCTACCT
* * * * * * *
943065 AGGGGTTCGCTCCCTATTGCTTCAGAGAGTAGAACTCGAATAATCTTCTGCTT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* *
943118 ACGGGTTCGCTCCCTCTTGCTTCAGGG-GTAGAACTCGAACAATATTCTACCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* *
943170 ACGGGTTCACTCCCTTTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* * *
943223 ATGGGTTCACTCTCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* ** * * * *
943276 ACTGGTTCGTTCCCTCTTACTTCA-GGAGTAGAACTTGGACAATCTTCTGCCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* * * *
943328 AC-AG-TC-CTCCCTCTTGCTT-AGGGAGTAAAAATCAAACAATCTTCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
943373 GGTGTGATTC
Statistics
Matches: 265, Mismatches: 39, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 30 0.11
50 2 0.01
51 1 0.00
52 74 0.28
53 132 0.50
54 17 0.06
55 7 0.03
56 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (53 bp):
ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
Found at i:943176 original size:105 final size:104
Alignment explanation
Indices: 943011--943372 Score: 401
Period size: 105 Copynumber: 3.5 Consensus size: 104
943001 TCTTCGAACG
* * *** *
943011 ACGGGTCCGCTCCCTCTTG-TTCAGGGATAAAGGAACTCGAACAATCTTCTAAAAAGGGGTTCGC
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGGT--A-GAACTCGAACAATCTTCTACCTACGGGTTCGC
* *
943075 TCCCTATTGCTTCAGAGAGTAGAACTCGAATAATCTTCTGCTT
63 TCCCTATTGCTTCAG-GAGTAGAACTCGAACAATCTTCTGCCT
* *
943118 ACGGGTTCGCTCCCTCTTGCTTCAGGGGTAGAACTCGAACAATATTCTACCTACGGGTTCACTCC
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGGTAGAACTCGAACAATCTTCTACCTACGGGTTCGCTCC
*
943183 CTTTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
66 CTATTGCTTCA-GGAGTAGAACTCGAACAATCTTCTGCCT
* * * * * *
943223 ATGGGTTCACTCTCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACTGGTTCGTTC
1 ACGGGTTCGCTCCCTCTTGCTTCAGGG-GTAGAACTCGAACAATCTTCTACCTACGGGTTCGCTC
* * * *
943288 CCTCTTACTTCAGGAGTAGAACTTGGACAATCTTCTGCCT
65 CCTATTGCTTCAGGAGTAGAACTCGAACAATCTTCTGCCT
* * * *
943328 AC-AG-TC-CTCCCTCTTGCTT-AGGGAGTAAAAATCAAACAATCTTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGG-GTAGAACTCGAACAATCTTCT
943373 GGTGTGATTC
Statistics
Matches: 223, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
101 23 0.10
102 12 0.05
103 2 0.01
104 1 0.00
105 115 0.52
106 44 0.20
107 18 0.08
108 8 0.04
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (104 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGGTAGAACTCGAACAATCTTCTACCTACGGGTTCGCTCC
CTATTGCTTCAGGAGTAGAACTCGAACAATCTTCTGCCT
Found at i:943902 original size:42 final size:42
Alignment explanation
Indices: 943812--944061 Score: 229
Period size: 42 Copynumber: 6.0 Consensus size: 42
943802 TATGGATAAC
* * * ***
943812 CCGAAGGATTTAAT-ATCTTGCTCGAAAGACTCAAAAAT-GA
1 CCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
* *
943852 CCCAAATGATTTAATCATCATGCTTGAAAGACTTACTGATGGA
1 -CCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
* * *
943895 ACGAATGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
1 CCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
* ** * * * *
943937 CCAAAAAACTTCATCATCATGATCGAAAGACTTACTGATGGC
1 CCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
* * * * *
943979 CCGAAGGACTTCATCGTCATGCTCGAAAGACTTACTGAT-TA
1 CCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
*
944020 CCTGAA-GAATTTAATCATCATGCTCGAAAGACTAACTGATGG
1 CC-GAATG-ATTTAATCATCATGCTCGAAAGACTTACTGATGG
944062 CACTTACTGA
Statistics
Matches: 171, Mismatches: 33, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
41 15 0.09
42 154 0.90
43 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (42 bp):
CCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
Found at i:944010 original size:22 final size:21
Alignment explanation
Indices: 943944--944011 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
943934 GGCCCAAAAA
*
943944 ACTTCATCATCATGATCGAAAG
1 ACTTCATC-TCATGCTCGAAAG
* * *
943966 ACTT-A-CTGATGGCCCGAAGG
1 ACTTCATCTCAT-GCTCGAAAG
943986 ACTTCATCGTCATGCTCGAAAG
1 ACTTCATC-TCATGCTCGAAAG
944008 ACTT
1 ACTT
944012 ACTGATTACC
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.31
21 2 0.06
22 16 0.46
23 3 0.09
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (21 bp):
ACTTCATCTCATGCTCGAAAG
Found at i:944062 original size:84 final size:84
Alignment explanation
Indices: 943860--944194 Score: 314
Period size: 84 Copynumber: 3.9 Consensus size: 84
943850 GACCCAAATG
* ** * * * *
943860 ATTTAATCATCATGCTTGAAAGACTTACTGATGGAACGAATGATTTAATCATCATGCTCAAAAGA
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
** * *
943925 CTTACTGATGGCCCAAAAA
66 CTTACTGATTACCCGAAGA
* * * *
943944 ACTTCATCATCATGATCGAAAGACTTACTGATGGCCCGAAGGACTTCATCGTCATGCTCGAAAGA
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
*
944009 CTTACTGATTACCTGAAGA
66 CTTACTGATTACCCGAAGA
* * * *
944028 ATTTAATCATCATGCTCGAAAGACTAACTGATGGCACTTACTGATGGATTTGCTTCACTACTATT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGC-C---C-GAAGGACTT-CATCA-T-C-A-T
* * ** *
944093 AGGT-G-AAGGCTTACAAATTACCCGAAGG
56 -GCTCGAAAGACTTACTGATTACCCGAAGA
* *
944121 ATTTAATCATCATGCTCGAAAGACTTACCGATGGCCCGAAGGACTTCATCATCATGCTTGAAAGA
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
944186 CTTACTGAT
66 CTTACTGAT
944195 GGCTCTTACT
Statistics
Matches: 199, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
82 2 0.01
83 2 0.01
84 110 0.55
85 2 0.01
86 1 0.01
87 4 0.02
88 8 0.04
89 8 0.04
90 3 0.02
91 1 0.01
92 2 0.01
93 52 0.26
94 2 0.01
95 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (84 bp):
ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
CTTACTGATTACCCGAAGA
Found at i:944159 original size:42 final size:42
Alignment explanation
Indices: 944113--944197 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
944103 TTACAAATTA
*
944113 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACCGATGG
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACCGATGG
* * *
944155 CCCGAAGGACTTCATCATCATGCTTGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACCGATGG
944197 C
1 C
944198 TCTTACTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (42 bp):
CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACCGATGG
Found at i:944187 original size:135 final size:135
Alignment explanation
Indices: 943978--944321 Score: 456
Period size: 135 Copynumber: 2.6 Consensus size: 135
943968 TTACTGATGG
* * ** * * *
943978 CCCGAAGGACTTCATCGTCATGCTCGAAAGACTTACTGATTACCTGAAGAATTTAATCATCATGC
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
944043 TCGAAAGACTAACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTAGGTGAAGGCTTACA
66 TCGAAAGACTAACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTAGGTGAAGGCTTACA
944108 AATTA
131 AATTA
* * *
944113 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACCGATGGCCCGAAGGACTTCATCATCATGC
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
* * * * * * *
944178 TTGAAAGACTTACTGATGGCTCTTACTGATGGGTTTGCTTTACTACTCTTCGGTGAAGGCTTACA
66 TCGAAAGACTAACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTAGGTGAAGGCTTACA
944243 AATTA
131 AATTA
* ** * * ** *
944248 -CTGAAACACTTAATCATCATGCACGAAAGCCTTACTGATGGATCAAAGGATTTCATCATCATGC
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
944312 TCGAAAGACT
66 TCGAAAGACT
944322 TACTAAGTGC
Statistics
Matches: 180, Mismatches: 29, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
134 62 0.34
135 118 0.66
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (135 bp):
CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
TCGAAAGACTAACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTAGGTGAAGGCTTACA
AATTA
Found at i:944502 original size:42 final size:41
Alignment explanation
Indices: 944438--944538 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
944428 AGGTCTTATG
* * * *
944438 GATGGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* * *
944479 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACA
944521 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
944539 AATTGTTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:952970 original size:98 final size:98
Alignment explanation
Indices: 952798--952993 Score: 356
Period size: 98 Copynumber: 2.0 Consensus size: 98
952788 GTGTATTACC
* *
952798 CTTAATCCAGTTATGTAATATGTCGAGTTATGCAAATGAGGTTATCATGCAATTTAATTGAATTA
1 CTTAATCCAATTATGTAATATGTCGAGTTATGCAAATGAGGTTATCATGCAATTTAATTGAATGA
* *
952863 TATGTTAACAAATGAGTCATGTAAAAATTCAAA
66 TATGCTAACAAATGAGTCAAGTAAAAATTCAAA
952896 CTTAATCCAATTATGTAATATGTCGAGTTATGCAAATGAGGTTATCATGCAATTTAATTGAATGA
1 CTTAATCCAATTATGTAATATGTCGAGTTATGCAAATGAGGTTATCATGCAATTTAATTGAATGA
952961 TATGCTAACAAATGAGTCAAGTAAAAATTCAAA
66 TATGCTAACAAATGAGTCAAGTAAAAATTCAAA
952994 GGTATGCATA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (98 bp):
CTTAATCCAATTATGTAATATGTCGAGTTATGCAAATGAGGTTATCATGCAATTTAATTGAATGA
TATGCTAACAAATGAGTCAAGTAAAAATTCAAA
Found at i:955171 original size:10 final size:10
Alignment explanation
Indices: 955156--955236 Score: 71
Period size: 10 Copynumber: 8.1 Consensus size: 10
955146 CATTTAAATG
955156 ATAAACGAAC
1 ATAAACGAAC
955166 ATAAACGAAC
1 ATAAACGAAC
*
955176 ACAAACGAAC
1 ATAAACGAAC
955186 --AAAC-ATA-
1 ATAAACGA-AC
*
955193 ATAAATGAAC
1 ATAAACGAAC
955203 ATAAACGAACAC
1 ATAAACG-A-AC
*
955215 AATAAACGAAT
1 -ATAAACGAAC
955226 ATAAACGAAC
1 ATAAACGAAC
955236 A
1 A
955237 ACACAAACAC
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 4 0.07
10 36 0.62
11 2 0.03
12 3 0.05
13 7 0.12
ACGTcount: A:0.62, C:0.19, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:955218 original size:23 final size:23
Alignment explanation
Indices: 955166--955236 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
955156 ATAAACGAAC
*
955166 ATAAACGAACACAAACGAACAAACATA
1 ATAAACGAACATAAACGAAC--AC--A
*
955193 ATAAATGAACATAAACGAACACA
1 ATAAACGAACATAAACGAACACA
*
955216 ATAAACGAATATAAACGAACA
1 ATAAACGAACATAAACGAACA
955237 ACACAAACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 20 0.50
25 2 0.05
27 18 0.45
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.11
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:955520 original size:14 final size:14
Alignment explanation
Indices: 955501--955557 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
955491 GCTCTATGTT
955501 CGAACATAAATGAA
1 CGAACATAAATGAA
955515 CGAACATAAATGAA
1 CGAACATAAATGAA
*
955529 AGAACATAAATGAA
1 CGAACATAAATGAA
*
955543 CGAACATAAACGAA
1 CGAACATAAATGAA
955557 C
1 C
955558 ATATAATCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:957592 original size:19 final size:19
Alignment explanation
Indices: 957565--957603 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
957555 TAATTAAGGC
*
957565 AATGTTCATTTATTGAGGT
1 AATGGTCATTTATTGAGGT
957584 AATGGTCATTTATTGAGGT
1 AATGGTCATTTATTGAGGT
957603 A
1 A
957604 GATAACAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (19 bp):
AATGGTCATTTATTGAGGT
Found at i:963323 original size:3 final size:3
Alignment explanation
Indices: 963309--963398 Score: 101
Period size: 3 Copynumber: 30.0 Consensus size: 3
963299 TTTTGCCCAT
* * * * * *
963309 TTA TTT TTA TTA TTA TTA TAA ATA TTA TAA TTG TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
963357 -TA TTA TTA TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
963399 CAAAACACCC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.03
3 67 0.94
4 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:974511 original size:12 final size:13
Alignment explanation
Indices: 974489--974517 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
974479 CCTGAAGAAA
974489 AAAAATGAAAATG
1 AAAAATGAAAATG
974502 AAAAAT-AAAATG
1 AAAAATGAAAATG
974514 AAAA
1 AAAA
974518 GAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:974513 original size:18 final size:17
Alignment explanation
Indices: 974486--974524 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
974476 ATGCCTGAAG
974486 AAAA-AAAATGAAAATGA
1 AAAATAAAATGAAAA-GA
974503 AAAATAAAATGAAAAGA
1 AAAATAAAATGAAAAGA
974520 AAAAT
1 AAAAT
974525 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (17 bp):
AAAATAAAATGAAAAGA
Found at i:974915 original size:18 final size:18
Alignment explanation
Indices: 974889--974926 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
974879 AAGATTATCT
*
974889 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
974907 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
974925 TT
1 TT
974927 CTTTCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:976477 original size:113 final size:111
Alignment explanation
Indices: 976334--976541 Score: 310
Period size: 113 Copynumber: 1.9 Consensus size: 111
976324 ATAGATCACC
*
976334 ATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAA-TTCATCTGAAGAACGAAGAAGAAGTTCA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTT-ATCTGAAG-ACGAAGAAGAAGTTCA
* *
976398 TAATGAGAAGAACTTGTTTAACATTTTGTTTGAATTCATTACTCGATGG
64 TAATGAGAAGAACTTGTTCAAC-CTTTGTTTGAATTCATTACTCGATGG
* * * *
976447 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAATAACTTATCTGAAGAGGAATAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGACGAAGAAGAAGTTCATA
*
976512 ATGATAAGAACTTGTTCAACCTTTGTTTGA
66 ATGAGAAGAACTTGTTCAACCTTTGTTTGA
976542 TTCTATCACA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 9 0.10
112 34 0.40
113 41 0.48
114 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (111 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGACGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTGTTTGAATTCATTACTCGATGG
Found at i:976511 original size:236 final size:235
Alignment explanation
Indices: 976098--976648 Score: 845
Period size: 236 Copynumber: 2.3 Consensus size: 235
976088 CATTCAATGG
*
976098 ATCAACTATTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
976163 AATGAGAAGAACTTGTTTAACCTTTAGCTCGAATTCGTCACTCGATGGATCAACTTTTGCAGAGA
66 AATGAGAAGAACTTGTTTAACATTTAGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGA
*
976228 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTC
131 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
976293 AACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCACC
196 AACC-TTTGCATGACTCTATCACAGAAGGAGATAGATCACC
* * *
976334 ATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAATTCATCTGAAGAACGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
976399 AATGAGAAGAACTTGTTTAACATTTTGTTTGAATTCATTACTCGATGGATCAACTTTTCCAGAGA
66 AATGAGAAGAACTTGTTTAACATTTAGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGA
* * * * *
976464 AAGTTCGTAATGAGAATAACTTATCTGAAGAGGAATAAGAAGTTCATAATGATAAGAACTTGTTC
131 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
** * *
976529 AACCTTTGTTTGATTCTATCACAGAAGGAGATAGATCAGC
196 AACCTTTGCATGACTCTATCACAGAAGGAGATAGATCACC
* * * * *
976569 ATCAACATTTCCAGAAG-TGTTCATAATAAGAAGAACTCATCTTAAGAAGGAA-AATAAGTTCAT
1 ATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
976632 AATGAGAAGAACTTGTT
66 AATGAGAAGAACTTGTT
976649 CAATCTTGCC
Statistics
Matches: 286, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
233 27 0.09
234 30 0.10
235 47 0.16
236 182 0.64
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (235 bp):
ATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTTAACATTTAGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGA
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTGCATGACTCTATCACAGAAGGAGATAGATCACC
Found at i:977001 original size:3 final size:3
Alignment explanation
Indices: 976995--977072 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
976985 ACTGTTTTTT
** * * *
976995 TTA TTA TTA TTA GAA TTG TTA TAA TTA TTA GTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
977042 TTA TTA TTA TTAA TAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
977073 CAAAACAGGC
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:978458 original size:17 final size:18
Alignment explanation
Indices: 978438--978475 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
978428 TTTTTAATTT
*
978438 TATATGTTTA-TTTTCAA
1 TATATATTTATTTTTCAA
978455 TATATATTTATTTTTCAA
1 TATATATTTATTTTTCAA
978473 TAT
1 TAT
978476 TAAGAAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATATTTATTTTTCAA
Found at i:979600 original size:27 final size:27
Alignment explanation
Indices: 979580--979662 Score: 148
Period size: 27 Copynumber: 3.1 Consensus size: 27
979570 GCCTCGCTCC
*
979580 CTAGTTACTCCCAAAGTGCCTCGTGCA
1 CTAGTTAGTCCCAAAGTGCCTCGTGCA
979607 CTAGTTAGTCCCAAAGTGCCTCGTGCA
1 CTAGTTAGTCCCAAAGTGCCTCGTGCA
*
979634 CTAGTTAGTCCCAAAGTGCCTTGTGCA
1 CTAGTTAGTCCCAAAGTGCCTCGTGCA
979661 CT
1 CT
979663 TGCTTAAGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (27 bp):
CTAGTTAGTCCCAAAGTGCCTCGTGCA
Found at i:981041 original size:16 final size:17
Alignment explanation
Indices: 981022--981053 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
981012 AAAACCTTAA
981022 AAAATAAATA-AAAAAG
1 AAAATAAATATAAAAAG
981038 AAAATAAATATAAAAA
1 AAAATAAATATAAAAA
981054 TGGCTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAATAAATATAAAAAG
Found at i:983480 original size:85 final size:85
Alignment explanation
Indices: 983358--983869 Score: 616
Period size: 85 Copynumber: 6.0 Consensus size: 85
983348 TACAATGCAG
* * * * * * *
983358 TTGATATGCCTTTGA-CATGAATGAAATCAAACTCGAAGGTTTTTGTTAACATATATCCATTCTC
1 TTGATATGCCCTTGAGC-TGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTC
*
983422 ACCTTGAGCTATGCTGTAAAT
65 GCCTTGAGCTATGCTGTAAAT
* * *
983443 TTGATATGCCATTGAGTTGAATGGAATCGAACCCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
* *
983508 CCTTGAGCTATACTATAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * * * *
983528 TTGATATTCCCTTGAGCTGAATGGAATCGAACTTGAAGGTTTTAGTTGATAGATATCCCTTATCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
* *
983593 CCTTGAGCTATGTTATAAAT
66 CCTTGAGCTATGCTGTAAAT
* ** *
983613 TTGATATGCCCTTGAGCTGAATGGAATTGAACTTAAAGGTTTTTGTTGACA-ATAGCCATTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
983677 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * **
983697 TCGATATGCCCTTGAGCTAAATGGAATC-AGACTTGAATTTTTTTGTTGACAGATAGCCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGGAATCGA-ACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTC
983761 GCCTTGAGCTATGCTGTAAAT
65 GCCTTGAGCTATGCTGTAAAT
* * * * * ** *
983782 TTAATATGCCCTTAAGCTAAATGTAATCAAACTCGAAGGTTTTCATTGACAGATAGCCCTTATCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
* * *
983847 CCTTGAACTATGCTATAATT
66 CCTTGAGCTATGCTGTAAAT
983867 TTG
1 TTG
983870 GTTGGAAGAT
Statistics
Matches: 369, Mismatches: 54, Indels: 8
0.86 0.13 0.02
Matches are distributed among these distances:
83 1 0.00
84 71 0.19
85 296 0.80
86 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (85 bp):
TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
CCTTGAGCTATGCTGTAAAT
Found at i:983768 original size:169 final size:170
Alignment explanation
Indices: 983360--983864 Score: 629
Period size: 169 Copynumber: 3.0 Consensus size: 170
983350 CAATGCAGTT
* * * * * * * * *
983360 GATATGCCTTTGA-CATGAATGAAATCAAACTCGAAGGTTTTTGTTAACATATATCCATTCTCAC
1 GATATGCCCTTGAGC-TAAATGGAATCGAACTTGAAGGTTTTTGTTGACAGATATCCCTTCTCGC
* * *
983424 CTTGAGCTATGCTGTAAATTTGATATGCCATTGAGTTGAATGGAATCGAACCCGAAGGTTTTTGT
65 CTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGT
* *
983489 TGACAGATAGCCCTTCTCGCCTTGAGCTATACTATAAATTT
130 TGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTC
* * * * *
983530 GATATTCCCTTGAGCTGAATGGAATCGAACTTGAAGGTTTTAGTTGATAGATATCCCTTATCGCC
1 GATATGCCCTTGAGCTAAATGGAATCGAACTTGAAGGTTTTTGTTGACAGATATCCCTTCTCGCC
* * * **
983595 TTGAGCTATGTTATAAATTTGATATGCCCTTGAGCTGAATGGAATTGAACTTAAAGGTTTTTGTT
66 TTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTT
* *
983660 GACA-ATAGCCATTCTCGCCTTGAGCTATGCTGTAAATTC
131 GACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTC
** *
983699 GATATGCCCTTGAGCTAAATGGAATC-AGACTTGAATTTTTTTGTTGACAGATAGCCCTTCTCGC
1 GATATGCCCTTGAGCTAAATGGAATCGA-ACTTGAAGGTTTTTGTTGACAGATATCCCTTCTCGC
* * * * * **
983763 CTTGAGCTATGCTGTAAATTTAATATGCCCTTAAGCTAAATGTAATCAAACTCGAAGGTTTTCAT
65 CTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGT
* *
983828 TGACAGATAGCCCTTATCGCCTTGAACTATGCTATAA
130 TGACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAA
983865 TTTTGGTTGG
Statistics
Matches: 284, Mismatches: 48, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
168 1 0.00
169 143 0.50
170 139 0.49
171 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (170 bp):
GATATGCCCTTGAGCTAAATGGAATCGAACTTGAAGGTTTTTGTTGACAGATATCCCTTCTCGCC
TTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTT
GACAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTC
Found at i:988938 original size:64 final size:64
Alignment explanation
Indices: 988870--989154 Score: 335
Period size: 64 Copynumber: 4.5 Consensus size: 64
988860 TTGAAGGTGT
* ** *
988870 ATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATGAA-ACATCGAATGCAATTCGTG
988933 C
64 C
*
988934 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCCTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCGTGC
* * *
988998 ATCGATGCATAAGTAGTGCATCGATGCTTCCCATTAATAATGAAACATCAAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCGTGC
* * * * ** **
989062 ATCGATGCATAAG-ACATACATCGATGCATCCCAGTAATAAT-ACAACATCGAATACCTTTTATG
1 ATCGATGCATAAGTA-GTGCATCGATGCATCCCATTAATAATGA-AACATCGAATGCAATTCGTG
989125 C
64 C
* * *
989126 ACCGATGCATCAGTAGTGAATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
989155 ACCTTCATTA
Statistics
Matches: 192, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.01
64 183 0.95
65 7 0.04
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCGTGC
Found at i:989902 original size:18 final size:15
Alignment explanation
Indices: 989850--989895 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
989840 GGGTATAATT
*
989850 GTCCTTCGGGACGTA
1 GTCCTTCGGGATGTA
989865 GTCCTTCGGGATGTA
1 GTCCTTCGGGATGTA
989880 GTCCTTCGGGATGTA
1 GTCCTTCGGGATGTA
989895 G
1 G
989896 GAGTCCTACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.13, C:0.22, G:0.35, T:0.30
Consensus pattern (15 bp):
GTCCTTCGGGATGTA
Found at i:993458 original size:64 final size:64
Alignment explanation
Indices: 993390--993610 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
993380 TTGAAGGTGT
* ** *
993390 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTAGTG
993453 C
64 C
* *
993454 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTAGTGC
* * * * **
993518 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACCTTTTA-TG
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAAT-GCAATTAGTG
993581 C
64 C
*
993582 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
993611 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
63 2 0.01
64 120 0.89
65 13 0.10
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTAGTGC
Found at i:994323 original size:15 final size:15
Alignment explanation
Indices: 994305--994337 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
994295 GAGGGTATAA
*
994305 TAGTCCTTTGGGATG
1 TAGTCCTTCGGGATG
994320 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
994335 TAG
1 TAG
994338 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.36
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:996887 original size:86 final size:84
Alignment explanation
Indices: 996711--996888 Score: 234
Period size: 86 Copynumber: 2.1 Consensus size: 84
996701 ACCCTAAAAA
* * *
996711 AACTAAATAATAAATAAATAAATATAAAAATGGCTAAATTAAAAAAATAAATGAAAAAAGAATAT
1 AACTAAATAATAAATAAATAAATATAAAAATGGCTAAATTAAAAAAAGAAATAAAAAAAAAATAT
**
996776 AAAAAAGTAAAAAATGGTC
66 AAAAAAGTAAAAAAAAGTC
* *
996795 ACCTAAA-AATAGA-AAATAAATATAAAATATGGCTAAATTAAAAAAAGAACATAAATGAAAAAA
1 AACTAAATAATAAATAAATAAATATAAAA-ATGGCTAAATTAAAAAAAGAA-ATAAA--AAAAAA
*
996858 ATATAAAAAAGTAAAAAAAAGTT
62 ATATAAAAAAGTAAAAAAAAGTC
996881 AACTAAAT
1 AACTAAAT
996889 TCAAAAAGAC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
82 14 0.17
83 25 0.31
84 10 0.12
86 31 0.39
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (84 bp):
AACTAAATAATAAATAAATAAATATAAAAATGGCTAAATTAAAAAAAGAAATAAAAAAAAAATAT
AAAAAAGTAAAAAAAAGTC
Found at i:999498 original size:17 final size:17
Alignment explanation
Indices: 999476--999510 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
999466 TCTCGAGTAC
999476 ATCATATGGTTCTATGA
1 ATCATATGGTTCTATGA
999493 ATCATATGGTTCTATGA
1 ATCATATGGTTCTATGA
999510 A
1 A
999511 ACACAGGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (17 bp):
ATCATATGGTTCTATGA
Found at i:1003743 original size:19 final size:19
Alignment explanation
Indices: 1003715--1003769 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1003705 ACTTTATTCT
* *
1003715 CTTTTTTTTATTTAAATTG
1 CTTTTATTTATTTAAATCG
1003734 CTTTTATTTATCTT-AATCG
1 CTTTTATTTAT-TTAAATCG
*
1003753 CTTTTA-CTATTTAAATC
1 CTTTTATTTATTTAAATC
1003770 TGATACTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 2 0.06
18 7 0.23
19 20 0.65
20 2 0.06
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.60
Consensus pattern (19 bp):
CTTTTATTTATTTAAATCG
Found at i:1004118 original size:23 final size:23
Alignment explanation
Indices: 1004088--1004143 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1004078 GCTTCGGGAA
1004088 AGAAGGAGAAAACAAACAAATCC
1 AGAAGGAGAAAACAAACAAATCC
1004111 AGAAGGAGAAAACAAACAAATCC
1 AGAAGGAGAAAACAAACAAATCC
*
1004134 AGAAGAAGAA
1 AGAAGGAGAA
1004144 TCGAATTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.62, C:0.14, G:0.20, T:0.04
Consensus pattern (23 bp):
AGAAGGAGAAAACAAACAAATCC
Found at i:1008293 original size:26 final size:25
Alignment explanation
Indices: 1008256--1008320 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1008246 AAAAAAGAGA
*
1008256 AAAAAAG-GGAAAAAAACAACAGTTC
1 AAAAAAGAAGAAAAAAA-AACAGTTC
* *
1008281 AAAAAAGAAGAAAAAAATACTGTTC
1 AAAAAAGAAGAAAAAAAAACAGTTC
*
1008306 GAAAAA-AAGAAAAAA
1 AAAAAAGAAGAAAAAA
1008321 TAAAAAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.26
25 18 0.51
26 8 0.23
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.09
Consensus pattern (25 bp):
AAAAAAGAAGAAAAAAAAACAGTTC
Found at i:1008294 original size:25 final size:24
Alignment explanation
Indices: 1008255--1008320 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
1008245 AAAAAAAGAG
* *
1008255 AAAAAAAGGGAAAAAAACAACAGTTC
1 AAAAAAA-AGAAAAAAA-TACAGTTC
*
1008281 AAAAAAGAAGAAAAAAATACTGTTC
1 AAAAAA-AAGAAAAAAATACAGTTC
*
1008306 GAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
1008321 TAAAAAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 9 0.26
25 11 0.31
26 14 0.40
27 1 0.03
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.09
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAATACAGTTC
Found at i:1008356 original size:30 final size:30
Alignment explanation
Indices: 1008283--1008356 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 30
1008273 AACAGTTCAA
*
1008283 AAAAGAAGAAAAAAATACTGTTCGAAAAAAAG
1 AAAAGAA-AAAAAAATACTATTC-AAAAAAAG
*
1008315 AAAA-AATAAAAAATAC-ATT-AAAAAAATGG
1 AAAAGAAAAAAAAATACTATTCAAAAAAA--G
1008344 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
1008357 GTGGTGTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 7 0.19
29 7 0.19
30 16 0.44
31 2 0.06
32 4 0.11
ACGTcount: A:0.73, C:0.04, G:0.11, T:0.12
Consensus pattern (30 bp):
AAAAGAAAAAAAAATACTATTCAAAAAAAG
Found at i:1010024 original size:19 final size:19
Alignment explanation
Indices: 1010002--1010050 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1009992 TCTCTTATTT
*
1010002 TTTATTTAAATTGCTTTTA
1 TTTATTTAAATCGCTTTTA
*
1010021 TTTATTTTAATCGCTTTTA
1 TTTATTTAAATCGCTTTTA
*
1010040 -CTATTTAAATC
1 TTTATTTAAATC
1010051 TCATACTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTATTTAAATCGCTTTTA
Found at i:1023561 original size:15 final size:15
Alignment explanation
Indices: 1023541--1023576 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1023531 CGCCGACGTT
1023541 ACTGCCACCAACATC
1 ACTGCCACCAACATC
* *
1023556 ACTGCCACCGATATC
1 ACTGCCACCAACATC
1023571 ACTGCC
1 ACTGCC
1023577 GCCGTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.44, G:0.11, T:0.17
Consensus pattern (15 bp):
ACTGCCACCAACATC
Found at i:1024788 original size:24 final size:24
Alignment explanation
Indices: 1024761--1024814 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1024751 AGCTGATGAA
1024761 TTAGTAGCTGTTGTTAGTTTTTCT
1 TTAGTAGCTGTTGTTAGTTTTTCT
1024785 TTAGTAGCTGTTGTTAGTTTTTCT
1 TTAGTAGCTGTTGTTAGTTTTTCT
1024809 TTAGTA
1 TTAGTA
1024815 ACTTTAGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (24 bp):
TTAGTAGCTGTTGTTAGTTTTTCT
Found at i:1024996 original size:9 final size:9
Alignment explanation
Indices: 1024984--1025022 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
1024974 AAATAAATTC
1024984 AATGGATTA
1 AATGGATTA
1024993 AATGTGGATTA
1 AA--TGGATTA
1025004 AATGGATT-
1 AATGGATTA
1025012 AATGGATTA
1 AATGGATTA
1025021 AA
1 AA
1025023 GTTTTTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.30
9 10 0.37
11 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (9 bp):
AATGGATTA
Found at i:1029292 original size:138 final size:138
Alignment explanation
Indices: 1029058--1029326 Score: 421
Period size: 138 Copynumber: 1.9 Consensus size: 138
1029048 AATAGAGTCA
* * * *
1029058 GGGTTTAGAGAACCATGAATAAATTCATCCTCAGTATCTATACCCCTATTTTCTGGACCTAGATG
1 GGGTTTACAGAACCAGGAATAAATTCATCCTCAGTATCAATACCCCTATTTTCTAGACCTAGATG
* * * *
1029123 GTTGGCAATAATTTCAGCGTCTAGCAGAAATGTCTTCCCCATGAGATAAGACTCTAGGGTAGTAA
66 GTTGACAATAATTTCAGCGTCTAGCAAAAATGTATTCCCCATGAGATAAGACTCTAGGGTAATAA
1029188 CCAAATCG
131 CCAAATCG
* *
1029196 GGGTTTACAGAACCAGGAATAAATTCATCCTCAGTATCAATACCCTTATTTTCTAGACTTAGATG
1 GGGTTTACAGAACCAGGAATAAATTCATCCTCAGTATCAATACCCCTATTTTCTAGACCTAGATG
* * *
1029261 GTTGACAATAATTTCAGTGTTTAGCAAAAATGTATTCCCCATGAGATAAGACTCTATGGTAATAA
66 GTTGACAATAATTTCAGCGTCTAGCAAAAATGTATTCCCCATGAGATAAGACTCTAGGGTAATAA
1029326 C
131 C
1029327 ACTATTAATA
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 118 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (138 bp):
GGGTTTACAGAACCAGGAATAAATTCATCCTCAGTATCAATACCCCTATTTTCTAGACCTAGATG
GTTGACAATAATTTCAGCGTCTAGCAAAAATGTATTCCCCATGAGATAAGACTCTAGGGTAATAA
CCAAATCG
Found at i:1033905 original size:34 final size:34
Alignment explanation
Indices: 1033862--1033973 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 34
1033852 GCGCAATAAG
* * *
1033862 CACTCTAGGTGCTATCATCAGAAACATAAATTTA
1 CACTCTAGGTGCAATCATCAGATACATAAATATA
* *
1033896 CACTCTAGGTGCAATCATCAGATACAGAAATATG
1 CACTCTAGGTGCAATCATCAGATACATAAATATA
* ** *
1033930 CACTCCAAATGCAATCATCAGATACATAAATATG
1 CACTCTAGGTGCAATCATCAGATACATAAATATA
*
1033964 CACTCCAGGT
1 CACTCTAGGT
1033974 ATCATCATAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (34 bp):
CACTCTAGGTGCAATCATCAGATACATAAATATA
Found at i:1041889 original size:206 final size:207
Alignment explanation
Indices: 1041518--1042032 Score: 650
Period size: 206 Copynumber: 2.5 Consensus size: 207
1041508 CAATTTATTA
*** *
1041518 GTTGTTTTCTTCTTTTGAATGCACAAAAAATTCTGGGAAATCTGCA-TTTTTCTATTTGGGATTG
1 GTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTCT-TTTGGGATTG
* *
1041582 AGGAAAAGTTTTAACTTGGATATCAATTAGCTTGAATCACAATATGTTGCTGATTTAGTTGTGTT
65 AGGAAAAG---TAACTTGGATATCAATTAGCTTGAACCACAATATATTGCTGATTTAGTTGTGTT
* * * *
1041647 GTTTTCTTTTGCACGAGCAAAGTTATTGATTTATAAGTTTAAGTCTCAAGCTTGTGTGTG-TTGT
127 GTTTTCTTTTACACGAGCAAAGTTATTGACTTATAAGTTTAAGTCCCAAGCTTGTGTGTGTTTCT
*
1041711 GGTTTTCAATTTGTAG
192 GATTTTCAATTTGTAG
1041727 GTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTATTTTCTGTTTGGGATT
1 GTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATT-TTTTCT-TTTGGGATT
* ** * *
1041792 GAGGGAAAGT-A-TT-GACTATCAATTTTCTTGAACCATAATATATTGTTGATTTAGTTGTGTTG
64 GAGGAAAAGTAACTTGGA-TATCAATTAGCTTGAACCACAATATATTGCTGATTTAGTTGTGTTG
** * *
1041854 TTTTCTTTTACGTGAGCAAAGTTATT-AGCTTATAAGTTTTAGTCCCATGCTTGTGTGTGTTTCT
128 TTTTCTTTTACACGAGCAAAGTTATTGA-CTTATAAGTTTAAGTCCCAAGCTTGTGTGTGTTTCT
**
1041918 GATTTTCAATTTGTTT
192 GATTTTCAATTTGTAG
* *
1041934 GTTGTTTTCTTCTTTTTAATGCATGCAAAATTCTGGGGAATCTGCATTTTTT-TTTTTGGATTGA
1 GTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTCTTTTGGGATTGA
1041998 GGAAAAGTCTTAACTT-GACTATCAATTAGCTTGAA
66 GGAAAAG---TAACTTGGA-TATCAATTAGCTTGAA
1042033 TCCAACTTAT
Statistics
Matches: 268, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
204 16 0.06
205 4 0.01
206 96 0.36
207 65 0.24
208 2 0.01
209 61 0.23
210 1 0.00
211 23 0.09
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (207 bp):
GTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTCTTTTGGGATTGA
GGAAAAGTAACTTGGATATCAATTAGCTTGAACCACAATATATTGCTGATTTAGTTGTGTTGTTT
TCTTTTACACGAGCAAAGTTATTGACTTATAAGTTTAAGTCCCAAGCTTGTGTGTGTTTCTGATT
TTCAATTTGTAG
Found at i:1044713 original size:2 final size:2
Alignment explanation
Indices: 1044706--1044734 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1044696 TCAATATACA
1044706 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
1044735 CAATAATTTA
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:1044907 original size:85 final size:85
Alignment explanation
Indices: 1044762--1044924 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 85
1044752 CAATCACGAC
* * * * * *
1044762 ACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACATGCAATGTAAGTCATACAT
1 ACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAAT
*
1044827 GCGTGTCATAAATTTATGAA
66 GCGCGTCATAAATTTATGAA
* * *
1044847 ACACAAATGTGTGTCATCTTAATTT-ATGATGGGGGCTTCAATGACGCGCAATG-AGCGTCATAA
1 ACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGTA-AGTCATAA
1044910 ATGCGCGTCATAAAT
64 ATGCGCGTCATAAAT
1044925 GCGTGTCATA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
84 1 0.02
85 62 0.94
86 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (85 bp):
ACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAAT
GCGCGTCATAAATTTATGAA
Found at i:1044917 original size:13 final size:13
Alignment explanation
Indices: 1044896--1044963 Score: 109
Period size: 13 Copynumber: 5.2 Consensus size: 13
1044886 AATGACGCGC
*
1044896 AATGAGCGTCATA
1 AATGCGCGTCATA
1044909 AATGCGCGTCATA
1 AATGCGCGTCATA
*
1044922 AATGCGTGTCATA
1 AATGCGCGTCATA
*
1044935 AATGCGTGTCATA
1 AATGCGCGTCATA
1044948 AATGCGCGTCATA
1 AATGCGCGTCATA
1044961 AAT
1 AAT
1044964 TCATGACGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1049900 original size:33 final size:33
Alignment explanation
Indices: 1049849--1049915 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1049839 AATAACAATG
* *
1049849 TTCCAAAGTTCAACTAAGAAGAAAATCTAACCA
1 TTCCAAAGTCCAAATAAGAAGAAAATCTAACCA
* *
1049882 TTCCAAAGTCCAAATAAGAAGACAATCTGACCA
1 TTCCAAAGTCCAAATAAGAAGAAAATCTAACCA
1049915 T
1 T
1049916 GGAAGATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.21
Consensus pattern (33 bp):
TTCCAAAGTCCAAATAAGAAGAAAATCTAACCA
Found at i:1058046 original size:28 final size:28
Alignment explanation
Indices: 1058006--1058070 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1057996 GACTCGACCC
* *
1058006 GACCCGGTCTAACCCAACTTGCCTGTCT
1 GACCCAGTCTAACCCAACTTGCATGTCT
1058034 GACCCAGTCTAACCCAACTTGCATGTCT
1 GACCCAGTCTAACCCAACTTGCATGTCT
1058062 GACCCAGTC
1 GACCCAGTC
1058071 CACCGTTGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (28 bp):
GACCCAGTCTAACCCAACTTGCATGTCT
Found at i:1063564 original size:15 final size:16
Alignment explanation
Indices: 1063546--1063579 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1063536 TAGAGTTTCC
1063546 TTTTGTTTAG-TTTAT
1 TTTTGTTTAGTTTTAT
*
1063561 TTTTGTTTTGTTTTAT
1 TTTTGTTTAGTTTTAT
1063577 TTT
1 TTT
1063580 GGTTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (16 bp):
TTTTGTTTAGTTTTAT
Found at i:1063606 original size:21 final size:21
Alignment explanation
Indices: 1063582--1063621 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1063572 TTTATTTTGG
1063582 TTATATATAGTATAGTTTTTT
1 TTATATATAGTATAGTTTTTT
1063603 TTATATATAGTATAGTTTT
1 TTATATATAGTATAGTTTT
1063622 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (21 bp):
TTATATATAGTATAGTTTTTT
Found at i:1063653 original size:44 final size:43
Alignment explanation
Indices: 1063604--1063719 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 43
1063594 TAGTTTTTTT
1063604 TATATATAGTATAGTTTTGAAAATAAATATAGCTGTGAAAAATA
1 TATATATAGTATAGTTTTGAAAATAAATATAGCT-TGAAAAATA
* * * *
1063648 TATATATAGTATAGTTTT-ATAAA-ACATAAAGCTTGGAATATA
1 TATATATAGTATAGTTTTGA-AAATAAATATAGCTTGAAAAATA
* *
1063690 TATATATAATAAAG-TTTGAAAATAAATATA
1 TATATATAGTATAGTTTTGAAAATAAATATA
1063720 TAAATTATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
41 6 0.10
42 25 0.41
43 9 0.15
44 21 0.34
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (43 bp):
TATATATAGTATAGTTTTGAAAATAAATATAGCTTGAAAAATA
Found at i:1063656 original size:21 final size:20
Alignment explanation
Indices: 1063605--1063656 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
1063595 AGTTTTTTTT
* *
1063605 ATATATAGTATAGTTTTGAAA
1 ATATATA-TATAGCTGTGAAA
1063626 ATA-A-ATATAGCTGTGAAAA
1 ATATATATATAGCTGTG-AAA
1063645 ATATATATATAG
1 ATATATATATAG
1063657 TATAGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.31
19 7 0.27
20 2 0.08
21 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (20 bp):
ATATATATATAGCTGTGAAA
Found at i:1063718 original size:22 final size:23
Alignment explanation
Indices: 1063693--1063742 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1063683 GAATATATAT
*
1063693 ATATAATAAAGT-TTGAAAATAA
1 ATATAATAAAGTATTAAAAATAA
* *
1063715 ATAT-ATAAATTATTAAAAATAT
1 ATATAATAAAGTATTAAAAATAA
1063737 ATATAA
1 ATATAA
1063743 ATATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAATAAAGTATTAAAAATAA
Found at i:1064880 original size:19 final size:19
Alignment explanation
Indices: 1064856--1064945 Score: 162
Period size: 19 Copynumber: 4.7 Consensus size: 19
1064846 TCTCTCTTTA
1064856 AAATGAAGAAATAGAGAAC
1 AAATGAAGAAATAGAGAAC
1064875 AAATGAAGAAATAGAGAAC
1 AAATGAAGAAATAGAGAAC
1064894 AAATGAAGAAATAGAGAAC
1 AAATGAAGAAATAGAGAAC
*
1064913 AAATGCAGAAATAGAGAAC
1 AAATGAAGAAATAGAGAAC
*
1064932 AAATGAGGAAATAG
1 AAATGAAGAAATAG
1064946 GGGTTTAGGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.61, C:0.06, G:0.22, T:0.11
Consensus pattern (19 bp):
AAATGAAGAAATAGAGAAC
Found at i:1070578 original size:24 final size:24
Alignment explanation
Indices: 1070566--1070661 Score: 65
Period size: 24 Copynumber: 3.9 Consensus size: 24
1070556 ATATAGAGAT
1070566 AAAAAGAAGAAAAAAAAAGAAGAG
1 AAAAAGAAGAAAAAAAAAGAAGAG
* *
1070590 AAAAAGAAAAAGAAGAAGGAAAAAAGAG
1 AAAAAGAAGAA-AA-AA--AAAGAAGAG
*
1070618 -AAAAG-AGAAAAGATAGAA-AAGA-
1 AAAAAGAAGAAAA-A-AAAAGAAGAG
*
1070640 AAAAACAGAGAAAAAAAAAGAA
1 AAAAAGA-AGAAAAAAAAAGAA
1070662 AAAATAAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
23 11 0.19
24 15 0.26
25 12 0.21
26 6 0.11
27 5 0.09
28 8 0.14
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (24 bp):
AAAAAGAAGAAAAAAAAAGAAGAG
Found at i:1070583 original size:14 final size:15
Alignment explanation
Indices: 1070566--1070658 Score: 77
Period size: 14 Copynumber: 6.3 Consensus size: 15
1070556 ATATAGAGAT
1070566 AAAAAGA-AG-AAAA
1 AAAAAGAGAGAAAAA
1070579 AAAAAGAAGAGAAAAA
1 AAAAAG-AGAGAAAAA
**
1070595 GAAAAAGA-AGAAGGA
1 -AAAAAGAGAGAAAAA
*
1070610 AAAAAGAGA-AAAGA
1 AAAAAGAGAGAAAAA
* *
1070624 GAAAAGATAGAAAAGA
1 AAAAAGAGAGAAAA-A
*
1070640 AAAAACAGAGAAAAA
1 AAAAAGAGAGAAAAA
1070655 AAAA
1 AAAA
1070659 GAAAAAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.09
14 19 0.30
15 16 0.25
16 17 0.27
17 6 0.09
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAAGAGAGAAAAA
Found at i:1070598 original size:21 final size:21
Alignment explanation
Indices: 1070572--1070665 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 21
1070562 AGATAAAAAG
1070572 AAGAAAAAAAAAGAAGAGAAA
1 AAGAAAAAAAAAGAAGAGAAA
*
1070593 AAG-AAAAAGAAGAAG-GAAAA
1 AAGAAAAAAAAAGAAGAG-AAA
* *
1070613 AAGAGAAAAGAGAA-AAGATAGAA
1 AAGA-AAAA-AAAAGAAGAGA-AA
* *
1070636 AAGAAAAAACAGAGAA-AAAAA
1 AAGAAAAAA-AAAGAAGAGAAA
1070657 AAGAAAAAA
1 AAGAAAAAA
1070666 TAAATCAAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
19 1 0.02
20 17 0.28
21 15 0.25
22 15 0.25
23 12 0.20
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAGAGAAA
Found at i:1070602 original size:30 final size:28
Alignment explanation
Indices: 1070566--1070665 Score: 107
Period size: 30 Copynumber: 3.5 Consensus size: 28
1070556 ATATAGAGAT
1070566 AAAAAGAAGAAAAAAAAAGAAGAGAAAAAG
1 AAAAAGAAGAAAAAAAAA-AAGAG-AAAAG
**
1070596 AAAAAGAAG-AAGGAAAAAAGAGAAAAG
1 AAAAAGAAGAAAAAAAAAAAGAGAAAAG
1070623 AGAAAAGATAGAAAAGAAAAAACAGAGAAAA-
1 A-AAAAGA-AGAAAA-AAAAAA-AGAGAAAAG
1070654 AAAAAGAA-AAAA
1 AAAAAGAAGAAAA
1070666 TAAATCAAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
27 6 0.10
28 15 0.25
29 9 0.15
30 17 0.28
31 6 0.10
32 8 0.13
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (28 bp):
AAAAAGAAGAAAAAAAAAAAGAGAAAAG
Found at i:1070614 original size:44 final size:40
Alignment explanation
Indices: 1070560--1070665 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 40
1070550 AAAAAAATAT
1070560 AGAGATAAAAAGAAGAAAAAAAAAGAAGAGAAAAAGAAAAAGA-
1 AGAGA-AAAAAGAAGAAAAAAAAAG-AGAG-AAAAGAAAAA-AC
*
1070603 AGAAGGAAAAAAG-AGAAAAGAGAAAAGATAGAAAAGAAAAAAC
1 AG-A-GAAAAAAGAAGAAAA-A-AAAAGAGAGAAAAGAAAAAAC
*
1070646 AGAGAAAAAAAAAGAAAAAA
1 AGAGAAAAAAGAAGAAAAAA
1070666 TAAATCAAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
40 1 0.02
41 8 0.15
42 8 0.15
43 20 0.36
44 11 0.20
45 7 0.13
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.02
Consensus pattern (40 bp):
AGAGAAAAAAGAAGAAAAAAAAAGAGAGAAAAGAAAAAAC
Found at i:1070623 original size:7 final size:7
Alignment explanation
Indices: 1070585--1070664 Score: 53
Period size: 7 Copynumber: 11.3 Consensus size: 7
1070575 AAAAAAAAAG
1070585 AAGAGAA
1 AAGAGAA
1070592 AA-AGAA
1 AAGAGAA
1070598 AA-AGAA
1 AAGAGAA
*
1070604 GAAGGAAAA
1 -AA-GAGAA
1070613 AAGAGAA
1 AAGAGAA
1070620 AAGAGAA
1 AAGAGAA
1070627 AAGATAGAA
1 AAG--AGAA
*
1070636 AAGAAAAA
1 AAG-AGAA
1070644 ACAGAGAA
1 A-AGAGAA
1070652 AA-A-AA
1 AAGAGAA
1070657 AAGA-AA
1 AAGAGAA
1070663 AA
1 AA
1070665 ATAAATCAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
5 4 0.07
6 16 0.26
7 19 0.31
8 10 0.16
9 12 0.20
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.01
Consensus pattern (7 bp):
AAGAGAA
Found at i:1070651 original size:16 final size:15
Alignment explanation
Indices: 1070572--1070663 Score: 69
Period size: 16 Copynumber: 5.8 Consensus size: 15
1070562 AGATAAAAAG
1070572 AAGAAAAAAAAAGAA
1 AAGAAAAAAAAAGAA
*
1070587 GAGAAAAAGAAAAAGAA
1 AAG-AAAA-AAAAAGAA
* *
1070604 GAAGGAAAAAAGAGAA
1 -AAGAAAAAAAAAGAA
* *
1070620 AAGAGAAAAGATAGAA
1 AAGA-AAAAAAAAGAA
*
1070636 AAGAAAAAACAGAGAA
1 AAGAAAAAA-AAAGAA
1070652 AA-AAAAAGAAAA
1 AAGAAAAA-AAAA
1070664 AATAAATCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
15 16 0.26
16 32 0.52
17 11 0.18
18 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:1072926 original size:257 final size:255
Alignment explanation
Indices: 1072423--1073317 Score: 1161
Period size: 258 Copynumber: 3.5 Consensus size: 255
1072413 GTTGATTTTC
* * *
1072423 AAAAAATGAGAAAGCAATTTCCAAAGTTTCTAATTTAA-GTCTTTTATGAAAATGAAATTTTTGA
1 AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGT-TTTCA-GAAAATGAAATTTTTGA
* ** *
1072487 AAAGTAAGAAAGCGGTTTTTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
64 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCTT
* * * * *
1072552 CGGGCCATCAGTAAATCTTTCGAGCATGATGATTAAATCTTTTGGGTCATATGT-AAGTCTTTCA
129 CGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAA-TCTTTCG
* *
1072616 AGCAAGATGATAAGTCCTTCAGGACATTCGTAATACCTTCGGATAGGATGTTTTCACATGAATTT
193 AGCAAGATGATAAGTCCTTCAGGCCA-TCTTAATACCTTCGG-TAGGATGTTTTCACATGAATTT
*
1072681 AAAAAAGGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
1 AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* * * *
1072746 AGTAAGAAAGTC-ATTTCCAAAGTTTCTTACCCAATAAATTATTTCCCAAATTGGTAAGTCCTTT
66 AGTAAGAAAG-CGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCTTC
* * * *
1072810 GGGTCATCAATAAGTATTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTCAATCTTTTGAG
130 GGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAATCTTTCGAG
* * * *
1072875 CAAGATGATAAGTCCTTCGGGCCATCCTTAAGACCTTCAGGTAGGATGTTTTCATATAAATTT
195 CAAGATGATAAGTCCTTCAGGCCAT-CTTAATACCTTC-GGTAGGATGTTTTCACATGAATTT
* * *
1072938 GAAAATTGAGAAAGCGATTTCCAAAATTTCTCATTTAGTAT-TTTTCAGAAAATGAAATTTTTGA
1 AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTA--ATGTTTTCAGAAAATGAAATTTTTGA
* *
1073002 AAAGTAAGAAAGCGATTTCAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
64 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCTT
* * * *
1073067 CGGGCTC-TCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTTGGATCATCTGTCAGTCTTTCG
129 CGGG-TCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAATCTTTCG
* * * * * * *
1073131 AGTAAGATGTTAAGTCCTTTAGGCCATCTATAATACCTTCGGGAAGAATTTTTTCACATGATTTT
193 AGCAAGATGATAAGTCCTTCAGGCCATCT-TAATACCTTC-GGTAGGATGTTTTCACATGA--AT
1073196 TT
254 TT
* * *
1073198 AAAAAAATGAGAAAGCGATTTTCAAAGTATCTCATTTAATATTTTCAGAAAATGAAATTTTTGAA
1 -AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAA
** * *
1073263 AAGTAAGAAAGTAATTTCCAAAGTTTCTTACCTAATAAACAATTTCCCAAATTGG
65 AAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGG
1073318 ACTATCAGTT
Statistics
Matches: 555, Mismatches: 68, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
256 1 0.00
257 214 0.39
258 224 0.40
259 8 0.01
260 76 0.14
261 32 0.06
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (255 bp):
AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
AGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCTTCG
GGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAATCTTTCGAGC
AAGATGATAAGTCCTTCAGGCCATCTTAATACCTTCGGTAGGATGTTTTCACATGAATTT
Found at i:1073104 original size:258 final size:257
Alignment explanation
Indices: 1072423--1073317 Score: 1144
Period size: 257 Copynumber: 3.5 Consensus size: 257
1072413 GTTGATTTTC
* * *
1072423 AAAAAATGAGAAAGCAATTTCCAAAGTTTCTAATTTAAGT-CTTTT-ATGAAAATGAAATTTTTG
1 AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTT-AGTATTTTTCA-GAAAATGAAATTTTTG
* ** *
1072486 AAAAGTAAGAAAGCGGTTTTTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCT
64 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCT
* * *
1072551 TCGGGC-CATCAGTAAATCTTTCGAGCATGATGATTAAATCTTTTGGGTCATATGT-AAGTCTTT
129 TCGGGCTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAA-TCTTT
* * * *
1072614 CAAGCAAGATGATAAGTCCTTCAGGACATTCGTAATACCTTCGGATAGGATGTTTTCACATGAAT
193 CGAGCAAGATGATAAGTCCTTCAGGCCA-TCTTAATACCTTCGG-TAGGATGTTTTCACATAAAT
1072679 TT
256 TT
*
1072681 AAAAAAGGAGAAAGCGATTTCCAAAGTTTCTCATTTA--ATGTTTTCAGAAAATGAAATTTTTGA
1 AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTAT-TTTTCAGAAAATGAAATTTTTGA
* * *
1072744 AAAGTAAGAAAGTC-ATTTCCAAAGTTTCTTACCCAATAAATTATTTCCCAAATTGGTAAGTCCT
65 AAAGTAAGAAAG-CGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCT
* * * * *
1072808 TTGGG-TCATCAATAAGTATTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTCAATCTTTT
129 TCGGGCTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAATCTTTC
* * *
1072872 GAGCAAGATGATAAGTCCTTCGGGCCATCCTTAAGACCTTCAGGTAGGATGTTTTCATATAAATT
194 GAGCAAGATGATAAGTCCTTCAGGCCAT-CTTAATACCTTC-GGTAGGATGTTTTCACATAAATT
1072937 T
257 T
* * *
1072938 GAAAATTGAGAAAGCGATTTCCAAAATTTCTCATTTAGTATTTTTCAGAAAATGAAATTTTTGAA
1 AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTCAGAAAATGAAATTTTTGAA
* *
1073003 AAGTAAGAAAGCGATTTCAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC
66 AAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCTTC
* * * *
1073068 GGGCTC-TCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTTGGATCATCTGTCAGTCTTTCGA
131 GGGCTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAATCTTTCGA
* * * * * * **
1073132 GTAAGATGTTAAGTCCTTTAGGCCATCTATAATACCTTCGGGAAGAATTTTTTCACATGATTTTT
196 GCAAGATGATAAGTCCTTCAGGCCATCT-TAATACCTTC-GGTAGGATGTTTTCACAT-A-AATT
1073197 T
257 T
* * *
1073198 AAAAAAATGAGAAAGCGATTTTCAAAGTATCTCATTTAATA-TTTTCAGAAAATGAAATTTTTGA
1 -AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTCAGAAAATGAAATTTTTGA
** * *
1073262 AAAGTAAGAAAGTAATTTCCAAAGTTTCTTACCTAATAAACAATTTCCCAAATTGG
65 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGG
1073318 ACTATCAGTT
Statistics
Matches: 553, Mismatches: 68, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
256 1 0.00
257 219 0.40
258 218 0.39
259 5 0.01
260 76 0.14
261 34 0.06
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (257 bp):
AAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTCAGAAAATGAAATTTTTGAA
AAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAATTGGTAAGTCCTTC
GGGCTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTGTCAATCTTTCGA
GCAAGATGATAAGTCCTTCAGGCCATCTTAATACCTTCGGTAGGATGTTTTCACATAAATTT
Found at i:1073716 original size:38 final size:38
Alignment explanation
Indices: 1073671--1074025 Score: 415
Period size: 38 Copynumber: 9.2 Consensus size: 38
1073661 GAAATTTCAA
*
1073671 TCAATCTTTGTTATTCTTGGCTTCCTCGTGAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
** * *
1073709 TTGATCTTCT-TTATTCTTGACTTCCTCATTAAGAGAAG
1 TCAATCTT-TGTTATTCTTGACTTCCTCGTGAAGAGAAG
1073747 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
1073785 TCAATATTTGTTATTCTTGACTTCGTCGTGAATAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
** * *
1073823 TTGATCTTTTTTATTCTTGACTTCATCGTGAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
1073861 TCAATCTTTCTTATTCTTGACTTTCTCGTGAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * * * *
1073899 ACAATCTTTGTTATTTTTGACCTCTTCATGAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
1073937 TTAATCTTTGTTATTCTTGACTTCCTCGTAAAGAGGAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *** *
1073975 TCAATCTTTCAATGTTATTCTTGACTTTCTCACAAAGAGGAG
1 TCAATC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAG
1074017 TCAATCTTT
1 TCAATCTTT
1074026 CGGTGTTGCT
Statistics
Matches: 269, Mismatches: 42, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.00
38 230 0.86
39 3 0.01
41 2 0.01
42 33 0.12
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (38 bp):
TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
Found at i:1073875 original size:114 final size:114
Alignment explanation
Indices: 1073671--1074025 Score: 458
Period size: 114 Copynumber: 3.1 Consensus size: 114
1073661 GAAATTTCAA
* *
1073671 TCAATCTTTGTTATTCTTGGCTTCCTCGTGAAGAGAAGTTGATCTTCTTTATTCTTGACTTCCTC
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTGATCTTTTTTATTCTTGACTTCCTC
* * *
1073736 ATTAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
66 GTAAAGAGAAGTCAATCTTTCTTATTCTTGACTTCCTCGTGAAGAGAAG
* * * *
1073785 TCAATATTTGTTATTCTTGACTTCGTCGTGAATAGAAGTTGATCTTTTTTATTCTTGACTTCATC
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTGATCTTTTTTATTCTTGACTTCCTC
* *
1073850 GTGAAGAGAAGTCAATCTTTCTTATTCTTGACTTTCTCGTGAAGAGAAG
66 GTAAAGAGAAGTCAATCTTTCTTATTCTTGACTTCCTCGTGAAGAGAAG
* * * * * * *
1073899 ACAATCTTTGTTATTTTTGACCTCTTCATGAAGAGAAGTTAATCTTTGTTATTCTTGACTTCCTC
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTGATCTTTTTTATTCTTGACTTCCTC
* * *** *
1073964 GTAAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTTCTCACAAAGAGGAG
66 GTAAAGAGAAGTCAATCTTTC----TTATTCTTGACTTCCTCGTGAAGAGAAG
1074017 TCAATCTTT
1 TCAATCTTT
1074026 CGGTGTTGCT
Statistics
Matches: 210, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
114 178 0.85
118 32 0.15
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (114 bp):
TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTGATCTTTTTTATTCTTGACTTCCTC
GTAAAGAGAAGTCAATCTTTCTTATTCTTGACTTCCTCGTGAAGAGAAG
Found at i:1074060 original size:44 final size:42
Alignment explanation
Indices: 1073945--1074065 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 42
1073935 AGTTAATCTT
* *
1073945 TGTTATTCTTGACTTCCTCGTAAAGAGGAGTCAATCTTTCAA
1 TGTTATTCTAGACTTTCTCGTAAAGAGGAGTCAATCTTTCAA
* ** **
1073987 TGTTATTCTTGACTTTCTCACAAAGAGGAGTCAATCTTTCGG
1 TGTTATTCTAGACTTTCTCGTAAAGAGGAGTCAATCTTTCAA
* *
1074029 TGTTGCTTCCTAGACTTTCTCGTGAAGAGGAGTCAAT
1 TGTT-ATT-CTAGACTTTCTCGTAAAGAGGAGTCAAT
1074066 GTCTTAGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 41 0.61
43 2 0.03
44 24 0.36
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (42 bp):
TGTTATTCTAGACTTTCTCGTAAAGAGGAGTCAATCTTTCAA
Found at i:1075122 original size:182 final size:182
Alignment explanation
Indices: 1074825--1075256 Score: 584
Period size: 182 Copynumber: 2.4 Consensus size: 182
1074815 GGTATTCATA
* * * * *
1074825 AAGAGCAGTGAAGCAAATCAAGT-TCGATTCTATCTTCCCTGAAGATCAACGAAGTGGGTCAAAA
1 AAGAGTAGTGAAGCAAATCAA-TCTTGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAA
* * * * * *
1074889 -TTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATACCAGTCTTCCCTTAGATCTGAT
65 TTTTTTATCGAATATGATCTCCCCTAAAGAATAGTGGAGCAGACCAGTCTTCCCTTAGATATGAT
** *
1074953 CTCTCCTAAAGAGTAGCA-AAACAGATTGTCATTTTCCATATTTAATATTCCTG
130 CTCTCCTAAAGAGTAGCAGAAA-AGATCATCATTTTCCAGATTTAATATTCCTG
* *
1075006 AAGAGTAGTGAAGCAAATCAATCTTGATTCAATTTTCCCTGAAGAGCAGCGAAGTGGATCAAAAT
1 AAGAGTAGTGAAGCAAATCAATCTTGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAAT
* *
1075071 TTTTTATCGAATATGATCTCCCTTAAAGAATAGTGGAGCAGACCCGTCTTCCCTTAGATATGATC
66 TTTTTATCGAATATGATCTCCCCTAAAGAATAGTGGAGCAGACCAGTCTTCCCTTAGATATGATC
* * *
1075136 TCTCCTAAAGAGTAGCAGAGAAGATCATCATTTTCCAGATTTGATCTTCCTG
131 TCTCCTAAAGAGTAGCAGAAAAGATCATCATTTTCCAGATTTAATATTCCTG
** * *
1075188 AAGAGTAGTGAAGCAAATCAATCTTGATTCAATCTT-CCTAGAAGAGCATTGAAGTGAATCACAA
1 AAGAGTAGTGAAGCAAATCAATCTTGATTCAATCTTCCCT-GAAGAGCAACGAAGTGGATCAAAA
1075252 TTTTT
65 TTTTT
1075257 CAGACCTGAC
Statistics
Matches: 221, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
180 1 0.00
181 58 0.26
182 160 0.72
183 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (182 bp):
AAGAGTAGTGAAGCAAATCAATCTTGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAAT
TTTTTATCGAATATGATCTCCCCTAAAGAATAGTGGAGCAGACCAGTCTTCCCTTAGATATGATC
TCTCCTAAAGAGTAGCAGAAAAGATCATCATTTTCCAGATTTAATATTCCTG
Found at i:1075468 original size:15 final size:16
Alignment explanation
Indices: 1075450--1075483 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1075440 TAGAGTTTCC
1075450 TTTTGTTTAGTT-TAT
1 TTTTGTTTAGTTATAT
*
1075465 TTTTGTTTTGTTATAT
1 TTTTGTTTAGTTATAT
1075481 TTT
1 TTT
1075484 GGTTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTTGTTTAGTTATAT
Found at i:1075545 original size:53 final size:51
Alignment explanation
Indices: 1075487--1075701 Score: 180
Period size: 53 Copynumber: 4.2 Consensus size: 51
1075477 ATATTTTGGT
*
1075487 TATATATAGTATAGTTTGAAAATAAGTATAGTTTTGAAATATATATATATATA
1 TATATATA-TATAGTTTGAAAATAA-TATAGTTTAGAAATATATATATATATA
*
1075540 TATATATAGTATAGTTTTGAAAATAAATATAATTTAG-AATATATATATATATA
1 TATATATA-TATAG-TTTGAAAAT-AATATAGTTTAGAAATATATATATATATA
* * * *
1075593 TAGTATA-AT-T--TTAGAAAAT-ATATAGCTTGGATATATATATATATATA
1 TA-TATATATATAGTTTGAAAATAATATAGTTTAGAAATATATATATATATA
* * * *
1075640 TATATATATATA-TAT--ATATAACATAGTTT-GAAAATAAATATATAGTATTA
1 TATATATATATAGTTTGAAAATAATATAGTTTAG-AAATATATATATA-TA-TA
*
1075690 AATATATATATA
1 TATATATATATA
1075702 ATATAATATA
Statistics
Matches: 136, Mismatches: 15, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
46 12 0.09
47 23 0.17
48 27 0.20
49 3 0.02
50 13 0.10
51 1 0.01
52 1 0.01
53 33 0.24
54 21 0.15
55 2 0.01
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (51 bp):
TATATATATATAGTTTGAAAATAATATAGTTTAGAAATATATATATATATA
Found at i:1075628 original size:2 final size:2
Alignment explanation
Indices: 1075623--1075659 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1075613 TATAGCTTGG
1075623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1075660 ACATAGTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1076396 original size:17 final size:17
Alignment explanation
Indices: 1076371--1076413 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1076361 AATAGTAGAG
*
1076371 AATATCAACTAGAAAAT
1 AATAACAACTAGAAAAT
1076388 AATAACAACTAGAAAAT
1 AATAACAACTAGAAAAT
1076405 AATAACAAC
1 AATAACAAC
1076414 AAACAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.63, C:0.14, G:0.05, T:0.19
Consensus pattern (17 bp):
AATAACAACTAGAAAAT
Found at i:1081427 original size:15 final size:16
Alignment explanation
Indices: 1081402--1081434 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1081392 TTTTATCTAT
1081402 CTTGCAATTTAATATA
1 CTTGCAATTTAATATA
*
1081418 CTTG-AATTTATTATA
1 CTTGCAATTTAATATA
1081433 CT
1 CT
1081435 ATGTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (16 bp):
CTTGCAATTTAATATA
Found at i:1081565 original size:9 final size:8
Alignment explanation
Indices: 1081550--1081592 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
1081540 CAAAATAAAG
1081550 TAAAAAAA
1 TAAAAAAA
1081558 TAAAAAAA
1 TAAAAAAA
1081566 T-AAAAAA
1 TAAAAAAA
*
1081573 TCAGAAAAA
1 T-AAAAAAA
1081582 TAACAAAAA
1 TAA-AAAAA
1081591 TA
1 TA
1081593 TGTAGCGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 7 0.23
8 10 0.33
9 13 0.43
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1081571 original size:16 final size:16
Alignment explanation
Indices: 1081550--1081592 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1081540 CAAAATAAAG
1081550 TAAAAAAATAAAAAAA
1 TAAAAAAATAAAAAAA
*
1081566 T-AAAAAATCAGAAAAA
1 TAAAAAAAT-AAAAAAA
1081582 TAACAAAAATA
1 TAA-AAAAATA
1081593 TGTAGCGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 7 0.30
16 8 0.35
17 2 0.09
18 6 0.26
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
TAAAAAAATAAAAAAA
Found at i:1083886 original size:27 final size:28
Alignment explanation
Indices: 1083838--1083892 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
1083828 TAAGAATTAT
1083838 AGAATATCCCCTAAAGTATAAAATGACC
1 AGAATATCCCCTAAAGTATAAAATGACC
*
1083866 AGAATA-CCCCTAAAGTGTAAAATGACC
1 AGAATATCCCCTAAAGTATAAAATGACC
1083893 TAAAGTATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.45, C:0.22, G:0.13, T:0.20
Consensus pattern (28 bp):
AGAATATCCCCTAAAGTATAAAATGACC
Found at i:1097447 original size:23 final size:23
Alignment explanation
Indices: 1097367--1097469 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 23
1097357 TCACTAAATA
*
1097367 GTGCATTGATGCA-TCCTTTGAAT
1 GTGCATCGATGCACTCC-TTGAAT
* * * *
1097390 ATGCATCGAT--ACACCTTTAAG
1 GTGCATCGATGCACTCCTTGAAT
*
1097411 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
*
1097434 GTGCATCGATGCACT-C-TG-CT
1 GTGCATCGATGCACTCCTTGAAT
*
1097454 GTGCATCGATACACTC
1 GTGCATCGATGCACTC
1097470 ATCGGGTTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 15 0.24
21 15 0.24
22 3 0.05
23 30 0.48
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:1099337 original size:21 final size:21
Alignment explanation
Indices: 1099311--1099353 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1099301 GGATTGAATT
1099311 TAGAACTTGGATTGATAAACA
1 TAGAACTTGGATTGATAAACA
1099332 TAGAACTTGGATTGATAAACA
1 TAGAACTTGGATTGATAAACA
1099353 T
1 T
1099354 TTTGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (21 bp):
TAGAACTTGGATTGATAAACA
Found at i:1100193 original size:65 final size:64
Alignment explanation
Indices: 1100111--1100237 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 64
1100101 ATTTCGAATG
* * * *
1100111 CATTTAGTGCACCGATGCACAAGCCATGCATCGATGCTTCCCTGAATATTTTGAAACATCAAATT
1 CATTCAGTGCACCGATGCACAAGACATGCATCAATGC-ACCCTGAATATTTTGAAACATCAAATT
* * **
1100176 CATTCAGTGCACTGATGCACAAGACATTCATCAATGCACCCTGGCTATTTTGAAACATCAAA
1 CATTCAGTGCACCGATGCACAAGACATGCATCAATGCACCCTGAATATTTTGAAACATCAAA
1100238 GAAGATTTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
64 22 0.41
65 32 0.59
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (64 bp):
CATTCAGTGCACCGATGCACAAGACATGCATCAATGCACCCTGAATATTTTGAAACATCAAATT
Found at i:1100250 original size:64 final size:64
Alignment explanation
Indices: 1100111--1100260 Score: 167
Period size: 64 Copynumber: 2.3 Consensus size: 64
1100101 ATTTCGAATG
* * * **
1100111 CATTTAGTGCACCGATGCACAAGCCATGCATCGATGCTTCCCTGAATATTTTGAAACATCAAATT
1 CATTT-GTGCACCGATGCACAAGACATGCATCAATGCTACCCTGAATATTTTGAAACATCAAAAA
* * * **
1100176 CATTCAGTGCACTGATGCACAAGACATTCATCAATGC-ACCCTGGCTATTTTGAAACATCAAAGA
1 CATT-TGTGCACCGATGCACAAGACATGCATCAATGCTACCCTGAATATTTTGAAACATCAAA-A
1100240 A
64 A
*
1100241 GATTTGTGCACCGATGCACA
1 CATTTGTGCACCGATGCACA
1100261 CCTCAGTGTA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
64 36 0.51
65 34 0.49
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (64 bp):
CATTTGTGCACCGATGCACAAGACATGCATCAATGCTACCCTGAATATTTTGAAACATCAAAAA
Found at i:1106875 original size:18 final size:18
Alignment explanation
Indices: 1106850--1106909 Score: 111
Period size: 18 Copynumber: 3.3 Consensus size: 18
1106840 TGTCAGAACC
1106850 GGTGATTGGGAGATTGTT
1 GGTGATTGGGAGATTGTT
*
1106868 GCTGATTGGGAGATTGTT
1 GGTGATTGGGAGATTGTT
1106886 GGTGATTGGGAGATTGTT
1 GGTGATTGGGAGATTGTT
1106904 GGTGAT
1 GGTGAT
1106910 GTTATTGTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.17, C:0.02, G:0.43, T:0.38
Consensus pattern (18 bp):
GGTGATTGGGAGATTGTT
Found at i:1109696 original size:32 final size:31
Alignment explanation
Indices: 1109603--1109710 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 31
1109593 ATTTAGCGAA
* **
1109603 ACCGAAAGCAACCTGAATCGAAATTAACACAA
1 ACCGAAAGCAACCTGAATCGAATTTAAC-CCG
* * *
1109635 ACCAAAAGAAATCC-GAACCGAATTTTAACCCG
1 ACCGAAAGCAA-CCTGAATCGAA-TTTAACCCG
*
1109667 ATCCGAAAGCAACCTGAATTGAATTTAACCCG
1 A-CCGAAAGCAACCTGAATCGAATTTAACCCG
1109699 ACCTGAAAGCAA
1 ACC-GAAAGCAA
1109711 TCCGAACGCA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
31 2 0.03
32 38 0.62
33 21 0.34
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (31 bp):
ACCGAAAGCAACCTGAATCGAATTTAACCCG
Found at i:1110536 original size:32 final size:31
Alignment explanation
Indices: 1110435--1110538 Score: 84
Period size: 32 Copynumber: 3.3 Consensus size: 31
1110425 AAACCGATAT
*
1110435 GATATTGATCCGACCC-AAAATCTAAACGATC
1 GATATTGACCCGACCCAAAAATC-AAACGATC
* * * * * *
1110466 TAGTGTTAACCTGACCCAAAAATCAACCAATGC
1 GA-TATTGACCCGACCCAAAAATCAAACGAT-C
* *
1110499 AATATTGACCCGACCCAAAAATCAATCGATCC
1 GATATTGACCCGACCCAAAAATCAAACGAT-C
1110531 GATATTGA
1 GATATTGA
1110539 TTCAAACCAA
Statistics
Matches: 55, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
31 1 0.02
32 46 0.84
33 8 0.15
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.22
Consensus pattern (31 bp):
GATATTGACCCGACCCAAAAATCAAACGATC
Found at i:1118911 original size:65 final size:62
Alignment explanation
Indices: 1118830--1118986 Score: 192
Period size: 61 Copynumber: 2.5 Consensus size: 62
1118820 GCAGGTTTAT
* * * * * *
1118830 ATTAGCACTAGTGTGTAAGGACACTAAGTGTATGTGGTGGACATGACCTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAA-GAC-CT-AGTGTAGGTGGTGGACAAGACCCTACGTATCATATCCGG
*
1118895 ATTAGCACTAGAGTGTAA-ACCTAGTGTAGGTGGTGGCCAAGACCCTACGTATCATATCCGG
1 ATTAGCACTAGAGTGTAAGACCTAGTGTAGGTGGTGGACAAGACCCTACGTATCATATCCGG
* *
1118956 ATTAGCACTAGAGCGTAAG-CTTAGTGTAGGT
1 ATTAGCACTAGAGTGTAAGACCTAGTGTAGGT
1118987 TTAACAATAC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
61 61 0.74
62 2 0.02
63 2 0.02
65 17 0.21
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (62 bp):
ATTAGCACTAGAGTGTAAGACCTAGTGTAGGTGGTGGACAAGACCCTACGTATCATATCCGG
Found at i:1120586 original size:95 final size:95
Alignment explanation
Indices: 1120441--1120639 Score: 292
Period size: 95 Copynumber: 2.1 Consensus size: 95
1120431 AAACTCTATG
* *
1120441 GTGTTGGTAACTGTTGAACTTTTTCCTTTGCATTTTGTACTGTCGATACCAAGAACACAAGTATA
1 GTGTTGGTAACTGTTGAACTTTTTCCTTTACATTTTGTACTGGCGATACCAAGAACACAAGTATA
*
1120506 AGACGAAGTTTTCCTTTGGGTTTCTCTGGC
66 AGACGAAGTTTTCATTTGGGTTTCTCTGGC
* ** * *
1120536 GTGTTGGTAAGTGTTGAGTTTTTTCCTTTACATTTTGTA-TAGGCTATACCAAGAACACAAGTCT
1 GTGTTGGTAACTGTTGAACTTTTTCCTTTACATTTTGTACT-GGCGATACCAAGAACACAAGTAT
* *
1120600 AAGACGAAGTTTTTATTTGGGTTTCTCTGGT
65 AAGACGAAGTTTTCATTTGGGTTTCTCTGGC
1120631 GTGTTGGTA
1 GTGTTGGTA
1120640 TCCATTTATT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
94 1 0.01
95 92 0.99
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (95 bp):
GTGTTGGTAACTGTTGAACTTTTTCCTTTACATTTTGTACTGGCGATACCAAGAACACAAGTATA
AGACGAAGTTTTCATTTGGGTTTCTCTGGC
Found at i:1123511 original size:2 final size:2
Alignment explanation
Indices: 1123504--1123559 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1123494 CAAAGCAAAA
1123504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1123546 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1123560 TAGTTAATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1127955 original size:59 final size:59
Alignment explanation
Indices: 1127863--1128444 Score: 792
Period size: 59 Copynumber: 9.9 Consensus size: 59
1127853 AAATTCAATA
* * * *
1127863 GGAAATTCATACAATTAGTATGATTTCCTTATCATTTTAGCACAATTACTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * * **
1127922 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCATACTTAGTGCCCTATAG
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * * *
1127981 GGAAATTCATACACTTAGTATGA-TTGCTTATCATGTTAGCA-ACTTAGTGCCGTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * *
1128038 GGAAATTCATACACTTAGTATGATTTCCTTATCAATTTAGCACACGAAGTTCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * * *
1128097 GGAAGTTCATACACTTAGTATGATTTCCTTATCAGTTTAGCACACGAAGTTCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * **
1128156 GGAAATTCAAACACTTAGTATGATTTCCTTATCATCTTAGCACACTTAA-TGTACTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC-TAAGTGCCCTATCT
* * *
1128215 GGAAATTCATACACTTAGTATGATTTCCTAATCAGTTTAGCACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * ***
1128274 GGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAGCACACGAAGTGTTATATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* * * *
1128333 GGAAATTCATAGACTTAGTATGATTTTCTTATCAGTTTAGCACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
* *
1128392 GGAAATTCATACACTTAGTATGATTTCCTTATTATTTTAGCACACTTAGTGCC
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCC
1128445 ATTTGGTAAT
Statistics
Matches: 465, Mismatches: 54, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
57 36 0.08
58 33 0.07
59 394 0.85
60 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
Found at i:1128982 original size:20 final size:21
Alignment explanation
Indices: 1128957--1129004 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1128947 ATGTTACCTG
*
1128957 GTATCGATACTACCTC-ATCA
1 GTATCGATACTAACTCAATCA
*
1128977 GTATCGATACTAATTCAATCA
1 GTATCGATACTAACTCAATCA
1128998 GTATCGA
1 GTATCGA
1129005 AACTTCTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (21 bp):
GTATCGATACTAACTCAATCA
Found at i:1135040 original size:58 final size:59
Alignment explanation
Indices: 1134946--1135172 Score: 335
Period size: 58 Copynumber: 4.0 Consensus size: 59
1134936 AAATTCAATA
* * *
1134946 GGAAATTCATACAATTAGTATGATTTCC-TATTATTTTAGCACACTTAATGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
* *
1135004 AGAAATTCATACACTTAGTAT-AATTCCTTATCATTTTAG--CACTTAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
1135060 GGAAATTCATACACTTAGTATGATTTCCTTAT-ATTTTAGCACACTTAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
**
1135118 GGAAATTCATACACTTAGTATGATTTCCTTATCAAATTAG--CACTTAGTG-CCTATC
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATC
1135173 ACACGAAGTG
Statistics
Matches: 155, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
56 49 0.32
57 23 0.15
58 78 0.50
59 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
Found at i:1135171 original size:114 final size:114
Alignment explanation
Indices: 1134946--1135515 Score: 443
Period size: 118 Copynumber: 4.8 Consensus size: 114
1134936 AAATTCAATA
1134946 GGAAATTCATACAATTAGTATGATTTCCTATTATTTTAGCACACTTAATGCCCTATCTAGAAATT
1 GGAAATTCATACAATTAGTATGATTTCCTATTATTTTAGCACACTTAATGCCCTATCTAGAAATT
**
1135011 CATACACTTAGTATAATTCCTTATCATTTTAGCACTTAGTGCCCTATCT
66 CATACACTTAGTATAATTCCTTATCAAATTAGCACTTAGTGCCCTATCT
* * *
1135060 GGAAATTCATACACTTAGTATGATTTCCT-TATATTTTAGCACACTTAGTGCCCTATCTGGAAAT
1 GGAAATTCATACAATTAGTATGATTTCCTAT-TATTTTAGCACACTTAATGCCCTATCTAGAAAT
* *
1135124 TCATACACTTAGTATGATTTCCTTATCAAATTAGCACTTAGTG-CCTATCACA
65 TCATACACTTAGTAT-AATTCCTTATCAAATTAGCACTTAGTGCCCTAT--CT
* * * * **** * *
1135176 CGAAGTGCCCTATCTAGAAATTCA-TACACTTAGTATGATTTCCTTATCAGTTTAGCACAC-AAA
1 GGAAAT--TC-A--TA-CAATT-AGT--A--T-G-ATTTCCT-ATTAT---TTTAGCACACTTAA
* * * **
1135239 GTGCCCTATCTGGAAATTCATACACTTAGTATTATTTCATTATCATTTTAGCACACTTAGTGCCC
49 -TGCCCTATCTAGAAATTCATACACTTAGTA-TAATTCCTTATCAAATTAG--CACTTAGTGCCC
1135304 TATCT
110 TATCT
* * * * *
1135309 GGAAATTCATACACTTAGTATGATTTCCTTATCAATTTAGCACAC-GAAGTGCCCTATCTGGAAA
1 GGAAATTCATACAATTAGTATGATTTCC-TATTATTTTAGCACACTTAA-TGCCCTATCTAGAAA
* ** * ***
1135373 TTCATACACTTAATATAATTTCCTTATCAGTTTAACAGAAGAAGTGCCCTATCT
64 TTCATACACTTAGTATAA-TTCCTTATCAAATTAGC--ACTTAGTGCCCTATCT
* * *
1135427 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACA-TGAAGTGCCCTATCT-GAAA
1 GGAAATTCATACAATTAGTATGATTTCC-TATTATTTTAGCACACTTAA-TGCCCTATCTAG-AA
*
1135490 ATTCATACACTTAGTATGATTTCCTT
63 ATTCATACACTTAGTAT-AATTCCTT
1135516 TATTTAGCAC
Statistics
Matches: 375, Mismatches: 46, Indels: 66
0.77 0.09 0.14
Matches are distributed among these distances:
113 1 0.00
114 79 0.21
115 24 0.06
116 6 0.02
117 3 0.01
118 150 0.40
119 2 0.01
121 6 0.02
122 6 0.02
123 2 0.01
124 1 0.00
125 1 0.00
126 2 0.01
127 5 0.01
128 5 0.01
129 3 0.01
130 2 0.01
131 2 0.01
132 55 0.15
133 6 0.02
134 9 0.02
135 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (114 bp):
GGAAATTCATACAATTAGTATGATTTCCTATTATTTTAGCACACTTAATGCCCTATCTAGAAATT
CATACACTTAGTATAATTCCTTATCAAATTAGCACTTAGTGCCCTATCT
Found at i:1135264 original size:59 final size:59
Alignment explanation
Indices: 1135172--1135527 Score: 547
Period size: 59 Copynumber: 6.1 Consensus size: 59
1135162 TAGTGCCTAT
*
1135172 CACACGAAGTGCCCTATCTAGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
1 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
* * * *
1135231 CACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATTATTTCATTATCATTTTAG
1 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
** *
1135290 CACACTTAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAATTTAG
1 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
* * *
1135349 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAATATAATTTCCTTATCAGTTTAA
1 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
* * *
1135408 CAGAAGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAG
1 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
* *
1135467 CACATGAAGTGCCCTATCTGAAAATTCATACACTTAGTATGATTTCCTT-T-A-TTTAG
1 CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
1135523 CACAC
1 CACAC
1135528 TTAGTGCTAT
Statistics
Matches: 271, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
56 9 0.03
57 1 0.00
58 1 0.00
59 260 0.96
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (59 bp):
CACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAGTTTAG
Done.