Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 3 of 19
Found at i:576013 original size:45 final size:45
Alignment explanation
Indices: 575949--576290 Score: 417
Period size: 45 Copynumber: 7.7 Consensus size: 45
575939 GCCAAGGCCA
** * * * * * *
575949 TCTCTTTCTTTGTCTTCTCAGATGAGCCATTCACTGTCACAGGCA
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCG
* * * * *
575994 TTTCTTTCTTCATCTTCTCAGCCGAGATATTTAGTGTCAAAGCCA
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCG
* *
576039 TGTCTTTCTTCATCTTCTCAGCTGAGCTATTTACAGTCAAAGCCG
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCG
576084 TCTCTTTCTTCATCTTCTCCA-CTGAGCTATTTACTGTCAAAGCCG
1 TCTCTTTCTTCATCTTCT-CAGCTGAGCTATTTACTGTCAAAGCCG
**
576129 TCTCTTTCTTCATCTTCTCAGCCAAGCTATTTACTGTCAAAGCCG
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCG
* * *
576174 TCTCTTTCTTCATCTTCTCAGCCGAGCTATTGACTG-C--AGCGG
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCG
*
576216 TCTCTTT-TCTCATCTTCTCAGCTGAGCTATTTACTGTC-ATGACCG
1 TCTCTTTCT-TCATCTTCTCAGCTGAGCTATTTACTGTCAAAG-CCG
*
576261 TCTCTTTCTTCATCATCTCAGCTGAGCTAT
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTAT
576291 CTATGGTCAC
Statistics
Matches: 261, Mismatches: 29, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.00
42 36 0.14
43 1 0.00
44 4 0.02
45 216 0.83
46 3 0.01
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.39
Consensus pattern (45 bp):
TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCG
Found at i:576312 original size:132 final size:134
Alignment explanation
Indices: 575996--576299 Score: 397
Period size: 132 Copynumber: 2.3 Consensus size: 134
575986 CACAGGCATT
* *
575996 TCTTTCTTCATCTTCTCAGCCGAGATATTTA-GTGTCAAAGCCATGTCTTTCTTCATCTTCTCAG
1 TCTTTCTTCATCTTCTCAGCCGAGCTATTTATG-GTCAAAGCCATCTCTTTCTTCATCTTCTCAG
* *
576060 CTGAGCTATTTACAGTCAAAGCCGTCTCTTTCTTCATCTTCTCCACTGAGCTATTTACTGTCAAA
65 CCGAGCTATTGACAGTC-AAGCCGTCTCTTTCTTCATCTTCTCCACTGAGCTATTTACTGTCAAA
576125 GCCGTC
129 GCCGTC
* *
576131 TCTTTCTTCATCTTCTCAGCCAAGCTATTTACT-GTCAAAGCCGTCTCTTTCTTCATCTTCTCAG
1 TCTTTCTTCATCTTCTCAGCCGAGCTATTTA-TGGTCAAAGCCATCTCTTTCTTCATCTTCTCAG
* *
576195 CCGAGCTATTGACTG-C-AGCGGTCTCTTT-TCTCATCTTCT-CAGCTGAGCTATTTACTGTC-A
65 CCGAGCTATTGACAGTCAAGCCGTCTCTTTCT-TCATCTTCTCCA-CTGAGCTATTTACTGTCAA
*
576255 TGACCGTC
128 AG-CCGTC
* * *
576263 TCTTTCTTCATCATCTCAGCTGAGCTATCTATGGTCA
1 TCTTTCTTCATCTTCTCAGCCGAGCTATTTATGGTCA
576300 CATTCATTTC
Statistics
Matches: 150, Mismatches: 13, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
131 6 0.04
132 73 0.49
134 1 0.01
135 70 0.47
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.39
Consensus pattern (134 bp):
TCTTTCTTCATCTTCTCAGCCGAGCTATTTATGGTCAAAGCCATCTCTTTCTTCATCTTCTCAGC
CGAGCTATTGACAGTCAAGCCGTCTCTTTCTTCATCTTCTCCACTGAGCTATTTACTGTCAAAGC
CGTC
Found at i:579552 original size:87 final size:87
Alignment explanation
Indices: 579406--579579 Score: 287
Period size: 87 Copynumber: 2.0 Consensus size: 87
579396 GAATAAGACA
* * *
579406 CTGGAAACTCAGAACCAGAGTTTGCATCATTGGGTGGCATAGTTTGAGAACTAGCTCTGAATCTA
1 CTGGAAACTCAAAAACAGAGTTTGCATCATTGGATGGCATAGTTTGAGAACTAGCTCTGAATCTA
579471 AGATGGGACAATATA-TCACAAG
66 AGATGGGACAATA-ACTCACAAG
*
579493 CTGGAAACTCAAAAACAGAGTTTGCATCATTGGATGGCGTAGTTTGAGAACTAGCTCTGAATCTA
1 CTGGAAACTCAAAAACAGAGTTTGCATCATTGGATGGCATAGTTTGAGAACTAGCTCTGAATCTA
*
579558 AGATGGGATAATAACTCACAAG
66 AGATGGGACAATAACTCACAAG
579580 TTAATAAGCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
86 1 0.01
87 80 0.99
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (87 bp):
CTGGAAACTCAAAAACAGAGTTTGCATCATTGGATGGCATAGTTTGAGAACTAGCTCTGAATCTA
AGATGGGACAATAACTCACAAG
Found at i:580540 original size:2 final size:2
Alignment explanation
Indices: 580533--580559 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
580523 CAAAAACAAG
580533 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
580560 CTTGCAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:586354 original size:71 final size:72
Alignment explanation
Indices: 586192--586376 Score: 191
Period size: 71 Copynumber: 2.6 Consensus size: 72
586182 TGTCAAGCTG
* * *
586192 TCTTCAAGGAAAGGTATCAATACCTAACCAACAAAATGCCCCAAGATGTATTCTATGTATAATGT
1 TCTTCAAGGAAGGGTATCGATACCTAACCAACAAAATGCCCCAAGATGTATTCTATGTAAAATGT
586257 ATCAATA
66 ATCAATA
* * * * * * *
586264 TCTT-AAGAAAGGATGTCGATACTTAACCAATAGAAA-GCCTCAAG-TAGTATTTTATGTAAAAT
1 TCTTCAAGGAAGGGTATCGATACCTAACCAACA-AAATGCCCCAAGAT-GTATTCTATGTAAAAT
586326 GTATCAATA
64 GTATCAATA
* * * *
586335 -CTTCATGGAAGGGTATCGATACCTCA-CAACCAAATTCCCCAA
1 TCTTCAAGGAAGGGTATCGATACCTAACCAACAAAATGCCCCAA
586377 AGGGCATTTT
Statistics
Matches: 89, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
69 3 0.03
70 12 0.13
71 67 0.75
72 7 0.08
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (72 bp):
TCTTCAAGGAAGGGTATCGATACCTAACCAACAAAATGCCCCAAGATGTATTCTATGTAAAATGT
ATCAATA
Found at i:586888 original size:2 final size:2
Alignment explanation
Indices: 586881--586919 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
586871 TGGCAGTCAT
* *
586881 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
586920 GAATAGCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:587420 original size:20 final size:19
Alignment explanation
Indices: 587395--587447 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
587385 AAATAAAAAA
*
587395 TCCTTTTTTTTTATTTTTTT
1 TCCTTTTTTTTT-TTTTTGT
587415 TCCTTTTTTTCATTTTTTTGT
1 TCCTTTTTTT--TTTTTTTGT
*
587436 TCATTTTTTTTT
1 TCCTTTTTTTTT
587448 CCATAGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 15 0.52
22 2 0.07
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (19 bp):
TCCTTTTTTTTTTTTTTGT
Found at i:587433 original size:12 final size:12
Alignment explanation
Indices: 587418--587447 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
587408 TTTTTTTTCC
587418 TTTTTTTCATTT
1 TTTTTTTCATTT
*
587430 TTTTGTTCATTT
1 TTTTTTTCATTT
587442 TTTTTT
1 TTTTTT
587448 CCATAGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTTCATTT
Found at i:591947 original size:62 final size:62
Alignment explanation
Indices: 591880--592000 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
591870 TCAAGAATTT
* *
591880 AGACAAAATACATCCAAAATTGTAACTAAATAGCTCTATAAATTGGAGTTATCAAAATACGC
1 AGACAAAATACATCCAAAATTATAACTAAATAACTCTATAAATTGGAGTTATCAAAATACGC
* *
591942 AGACAAAATACATCCAAAATTATAACTAAATAACTCTATAAATTGGGGTTATCAGAATA
1 AGACAAAATACATCCAAAATTATAACTAAATAACTCTATAAATTGGAGTTATCAAAATA
592001 TGCAATCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (62 bp):
AGACAAAATACATCCAAAATTATAACTAAATAACTCTATAAATTGGAGTTATCAAAATACGC
Found at i:612118 original size:15 final size:15
Alignment explanation
Indices: 612084--612128 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
612074 TAATTAATAA
*
612084 TTTAAATATTAACATT
1 TTTAAATATTAA-TTT
612100 TTTAAATATTAATTT
1 TTTAAATATTAATTT
612115 TTTATAAT-TTAATT
1 TTTA-AATATTAATT
612129 ATTAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATATTAATTT
Found at i:612122 original size:38 final size:42
Alignment explanation
Indices: 612061--612175 Score: 129
Period size: 38 Copynumber: 2.9 Consensus size: 42
612051 TTATAATTTA
612061 TTTAAAATACTAATAA-TTA---ATAATTTAAATATTAACATT
1 TTTAAAATACT-ATAATTTATTTATAATTTAAATATTAACATT
* **
612100 TTT-AAATA-T-TAATTT-TTTATAATTTAATTATTAATTTT
1 TTTAAAATACTATAATTTATTTATAATTTAAATATTAACATT
612138 TTTAAAATACTAATAATTTATTTATAATTTAAATATTA
1 TTTAAAATACT-ATAATTTATTTATAATTTAAATATTA
612176 TTATGATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
35 3 0.05
36 2 0.03
37 1 0.02
38 25 0.40
39 8 0.13
40 1 0.02
42 6 0.10
43 17 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (42 bp):
TTTAAAATACTATAATTTATTTATAATTTAAATATTAACATT
Found at i:612131 original size:22 final size:22
Alignment explanation
Indices: 612100--612175 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
612090 TATTAACATT
612100 TTTAAATATTAATTTTTTATAA
1 TTTAAATATTAATTTTTTATAA
*
612122 TTTAATTATTAATTTTTT-TAA
1 TTTAAATATTAATTTTTTATAA
** * *
612143 AAT-ACTAATAATTTATTTATAA
1 TTTAAATATTAATTT-TTTATAA
612165 TTTAAATATTA
1 TTTAAATATTA
612176 TTATGATTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 9 0.21
21 7 0.17
22 21 0.50
23 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAATATTAATTTTTTATAA
Found at i:612151 original size:24 final size:23
Alignment explanation
Indices: 612106--612160 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
612096 CATTTTTAAA
* *
612106 TATTAA-TTTTTTATAATTTAAT
1 TATTAATTTTTTTAAAATCTAAT
612128 TATTAATTTTTTTAAAATACTAAT
1 TATTAATTTTTTTAAAAT-CTAAT
* *
612152 AATTTATTT
1 TATTAATTT
612161 ATAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 6 0.22
23 10 0.37
24 11 0.41
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTAATTTTTTTAAAATCTAAT
Found at i:612186 original size:43 final size:42
Alignment explanation
Indices: 612061--612199 Score: 132
Period size: 43 Copynumber: 3.5 Consensus size: 42
612051 TTATAATTTA
**
612061 TTTAAAATACTAATAA-TTA---ATAATTTAAATATTAACAT
1 TTTAAAATACTAATAATTTATTTATAATTTAAATATTATTAT
* * *
612099 TTTTAAATA-T--TAATTT-TTTATAATTTAATTATTAATTTT
1 TTTAAAATACTAATAATTTATTTATAATTTAAATATT-ATTAT
612138 TTTAAAATACTAATAATTTATTTATAATTTAAATATTATTAT
1 TTTAAAATACTAATAATTTATTTATAATTTAAATATTATTAT
* * *
612180 GATTAAAATATTAAAAATTT
1 -TTTAAAATACTAATAATTT
612200 TAATTAATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
35 3 0.04
36 2 0.03
37 1 0.01
38 21 0.26
39 10 0.12
40 1 0.01
42 10 0.12
43 32 0.40
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (42 bp):
TTTAAAATACTAATAATTTATTTATAATTTAAATATTATTAT
Found at i:612407 original size:9 final size:8
Alignment explanation
Indices: 612383--612416 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
612373 TTTATTTTCA
612383 TTAAAATT
1 TTAAAATT
612391 TTAAAATT
1 TTAAAATT
*
612399 TTAAAAAT
1 TTAAAATT
612407 TTAATAATT
1 TTAA-AATT
612416 T
1 T
612417 ATTACTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTAAAATT
Found at i:612593 original size:8 final size:8
Alignment explanation
Indices: 612580--612620 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
612570 CATTATTATG
612580 ATTAAAAT
1 ATTAAAAT
612588 ATTAAAAT
1 ATTAAAAT
612596 ATTAATAAT
1 ATTAA-AAT
612605 -TTCAAAAT
1 ATT-AAAAT
612613 ATTAAAAT
1 ATTAAAAT
612621 TATTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTAAAAT
Found at i:613012 original size:18 final size:20
Alignment explanation
Indices: 612979--613015 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
612969 TGTGAAAAGG
612979 AAGAGAAAGAAGAAGGAAAA
1 AAGAGAAAGAAGAAGGAAAA
612999 AAGA-AAAGAA-AAGGAAA
1 AAGAGAAAGAAGAAGGAAA
613016 GTATTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (20 bp):
AAGAGAAAGAAGAAGGAAAA
Found at i:615991 original size:15 final size:15
Alignment explanation
Indices: 615961--616012 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
615951 ATCTTATTGC
615961 TTTAATTTTTAATTAA
1 TTTAA-TTTTAATTAA
*
615977 TTTAATTTTAGTTAA
1 TTTAATTTTAATTAA
615992 -TTAA-TTTAATT-A
1 TTTAATTTTAATTAA
616004 TTTGAATTT
1 TTT-AATTT
616013 GATTGTTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 1 0.03
13 8 0.26
14 6 0.19
15 11 0.35
16 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (15 bp):
TTTAATTTTAATTAA
Found at i:616275 original size:71 final size:71
Alignment explanation
Indices: 616154--616302 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
616144 TAACTGGCAT
* * * * *
616154 ACTACCAAGGGAATATGATTTAGTGCATTCAACCATTGACCTTAATCATAAGATAGTGCTATTTC
1 ACTATCAAGGGAACATGATTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTC
616219 CCCATC
66 CCCATC
*
616225 ACTATCAAGGGAACATGGTTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTC
1 ACTATCAAGGGAACATGATTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTC
*
616290 CCCTTC
66 CCCATC
616296 ACTATCA
1 ACTATCA
616303 GGAGCATATG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (71 bp):
ACTATCAAGGGAACATGATTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTC
CCCATC
Found at i:616314 original size:71 final size:70
Alignment explanation
Indices: 616161--616373 Score: 228
Period size: 71 Copynumber: 3.0 Consensus size: 70
616151 CATACTACCA
* * * * *
616161 AGGGAATATGATTTAGTGCATTCAACCATTGACCTTAATCATAAGATAGTGCTATTTCCCCATCA
1 AGGGAATATGGTTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTCCCCTTCA
616226 CTATC
66 CTATC
*
616231 AAGGGAACATGGTTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTCCCCTTC
1 -AGGGAATATGGTTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTCCCCTTC
616296 ACTATC
65 ACTATC
* ** * * ** * * * * * * *
616302 AGGAGCATATGGTCCATTGCATTTAGGCACTAATCTTAATAATAGGATCATGATATTTTCCTTTC
1 AGG-GAATATGGTTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTCCCCTTC
616367 ACTATC
65 ACTATC
616373 A
1 A
616374 AAGGAATACA
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
70 3 0.03
71 117 0.98
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (70 bp):
AGGGAATATGGTTTAGTGCATTCAACCACTAACCTTAATCATAAGATAATGCTATTTCCCCTTCA
CTATC
Found at i:619091 original size:20 final size:20
Alignment explanation
Indices: 619068--619106 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
619058 ACAAAATAAA
619068 TAACATAAAACT-AACATTAT
1 TAACATAAAA-TAAACATTAT
*
619088 TAACTTAAAATAAACATTA
1 TAACATAAAATAAACATTA
619107 AAATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (20 bp):
TAACATAAAATAAACATTAT
Found at i:620014 original size:32 final size:32
Alignment explanation
Indices: 619946--620016 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
619936 ATCATATATG
* * **
619946 CCAAGGTGCAGTGGGGTTTATACATTGTCAGT
1 CCAAGGTGCAATGGGGTTTATACATTGCCAAC
*
619978 CCAAGGTGCAATGTGGTTTATACATTGCCAAC
1 CCAAGGTGCAATGGGGTTTATACATTGCCAAC
620010 CCAAGGT
1 CCAAGGT
620017 TGATGGAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (32 bp):
CCAAGGTGCAATGGGGTTTATACATTGCCAAC
Found at i:624567 original size:12 final size:13
Alignment explanation
Indices: 624540--624601 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
624530 AGTTAACAAT
624540 AGAAAATAGAAAA-
1 AGAAAA-AGAAAAG
624553 AGAAAAGAGAAAAG
1 AGAAAA-AGAAAAG
*
624567 A-AAAAA-TAAAG
1 AGAAAAAGAAAAG
624578 AAGAAAAA-AAGAAG
1 -AGAAAAAGAA-AAG
624592 AGAAAAAGAA
1 AGAAAAAGAA
624602 TAAACATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.10
12 2 0.05
13 29 0.71
14 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AGAAAAAGAAAAG
Found at i:624572 original size:27 final size:27
Alignment explanation
Indices: 624542--624598 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
624532 TTAACAATAG
*
624542 AAAATAGAAAAAG-AAAAGAGAAAAGAA
1 AAAATA-AAAAAGAAAAAAAGAAAAGAA
* *
624569 AAAATAAAGAAGAAAAAAAGAAGAGAA
1 AAAATAAAAAAGAAAAAAAGAAAAGAA
624596 AAA
1 AAA
624599 GAATAAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (27 bp):
AAAATAAAAAAGAAAAAAAGAAAAGAA
Found at i:624579 original size:11 final size:11
Alignment explanation
Indices: 624549--624601 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
624539 TAGAAAATAG
624549 AAAAAGAA-AA
1 AAAAAGAAGAA
624559 GAGAAAAGAA-AA
1 -A-AAAAGAAGAA
624571 AATAAAGAAGAA
1 AA-AAAGAAGAA
*
624583 AAAAAGAAGAG
1 AAAAAGAAGAA
624594 AAAAAGAA
1 AAAAAGAA
624602 TAAACATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.63
12 13 0.34
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:624582 original size:19 final size:18
Alignment explanation
Indices: 624547--624601 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
624537 AATAGAAAAT
624547 AGAAAAAGAAAAGAGAAA
1 AGAAAAAGAAAAGAGAAA
*
624565 AGAAAAA-ATAAAGA-AGA
1 AGAAAAAGA-AAAGAGAAA
*
624582 A-AAAAAGAAGAGA-AAA
1 AGAAAAAGAAAAGAGAAA
624598 AGAA
1 AGAA
624602 TAAACATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 12 0.39
17 7 0.23
18 12 0.39
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AGAAAAAGAAAAGAGAAA
Found at i:624583 original size:32 final size:35
Alignment explanation
Indices: 624549--624625 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 35
624539 TAGAAAATAG
*
624549 AAAAAGAAAAGAGAAAAGAA-AAA-ATAAAGAAGAA
1 AAAAAGAAGAGA-AAAAGAATAAACATAAAGAAGAA
*
624583 AAAAAGAAGAGAAAAAGAATAAACATAAATAA-AA
1 AAAAAGAAGAGAAAAAGAATAAACATAAAGAAGAA
624617 TAAAAAGAA
1 -AAAAAGAA
624626 TTGAAACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 16 0.42
35 15 0.39
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.06
Consensus pattern (35 bp):
AAAAAGAAGAGAAAAAGAATAAACATAAAGAAGAA
Found at i:631606 original size:14 final size:14
Alignment explanation
Indices: 631589--631628 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
631579 AATAAAGTTT
631589 AAACAATAAAAACA
1 AAACAATAAAAACA
*
631603 AAACAAAAAAAACA
1 AAACAATAAAAACA
* *
631617 AGAGAATAAAAA
1 AAACAATAAAAA
631629 AGAAGATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.80, C:0.10, G:0.05, T:0.05
Consensus pattern (14 bp):
AAACAATAAAAACA
Found at i:631627 original size:15 final size:14
Alignment explanation
Indices: 631591--631642 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
631581 TAAAGTTTAA
* *
631591 ACAATAAAAACAAA
1 ACAAAAAAAACAAG
631605 ACAAAAAAAACAAG
1 ACAAAAAAAACAAG
* *
631619 AGAATAAAAAAGAAG
1 ACAA-AAAAAACAAG
*
631634 ATAAAAAAA
1 ACAAAAAAA
631643 CTCAAGAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.79, C:0.08, G:0.08, T:0.06
Consensus pattern (14 bp):
ACAAAAAAAACAAG
Found at i:632600 original size:25 final size:25
Alignment explanation
Indices: 632544--632600 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
632534 GGTGACAGGT
632544 AGAGTTTGAGTGTGGTTTTGGAAAA
1 AGAGTTTGAGTGTGGTTTTGGAAAA
*
632569 AGGGTTTGAGTGTGGTTTT-GAAAA
1 AGAGTTTGAGTGTGGTTTTGGAAAA
632593 ATGAGTTT
1 A-GAGTTT
632601 CACCGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (25 bp):
AGAGTTTGAGTGTGGTTTTGGAAAA
Found at i:640725 original size:21 final size:22
Alignment explanation
Indices: 640687--640728 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
640677 TTATTAATTT
640687 TAAAAATTTATTTAATTTAAAA
1 TAAAAATTTATTTAATTTAAAA
640709 TAAAAATTTATTT-ATTTAAA
1 TAAAAATTTATTTAATTTAAA
640729 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAAATTTATTTAATTTAAAA
Found at i:650430 original size:178 final size:177
Alignment explanation
Indices: 650125--650446 Score: 452
Period size: 178 Copynumber: 1.8 Consensus size: 177
650115 TGAAATATCT
* * * *
650125 TTGGATTAGTTATTGATTGACTTCTGAGTCATCCTATGAATTCACTGGTTATAGCAGTTATTAAC
1 TTGGATCAGTTATTCATTGACTTCTGAGTCATCCTATAAATTCACTGGTTATAGCAGTTATGAAC
* * * * * * *
650190 AAGGCACAATATGCATAGATCTGCAATTCTAAGCAATAATTGGAATACAACAATGCAGTAAGATT
66 AACGCACAACATGCAGACATCTGCAATTCTAAGCAATAATTAGAAGACAACAATGAAGTAAGATT
* *
650255 ATGTTCTGTTTCTAAGATTAAAAAATTGCAGTTCTTTTGCAATATAC
131 ATATTCTGGTTCTAAGATTAAAAAATTGCAGTTCTTTTGCAATATAC
650302 TTGGATCAGTTATTTCATTGACTTCTGAGTCATACC-ATAAATTCACTGGTTATAGCAGTTATGA
1 TTGGATCAGTTA-TTCATTGACTTCTGAGTCAT-CCTATAAATTCACTGGTTATAGCAGTTATGA
* *
650366 AC-ACGCACAACATGCAGACATCTGCAATTCTAAGCGATAATTTATAAGACAA-ATATGAAGTAA
64 ACAACGCACAACATGCAGACATCTGCAATTCTAAGCAATAA-TTAGAAGACAACA-ATGAAGTAA
650429 GATTATATTCTGGTTCTA
127 GATTATATTCTGGTTCTA
650447 GATAGAAGGG
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
177 45 0.36
178 79 0.63
179 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (177 bp):
TTGGATCAGTTATTCATTGACTTCTGAGTCATCCTATAAATTCACTGGTTATAGCAGTTATGAAC
AACGCACAACATGCAGACATCTGCAATTCTAAGCAATAATTAGAAGACAACAATGAAGTAAGATT
ATATTCTGGTTCTAAGATTAAAAAATTGCAGTTCTTTTGCAATATAC
Found at i:652722 original size:27 final size:27
Alignment explanation
Indices: 652684--652738 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
652674 TAGTCTGCCA
652684 AAAGACTGGTTTTTCACTCACTAGCAG
1 AAAGACTGGTTTTTCACTCACTAGCAG
652711 AAAGACTGGTTTTTCACTCACTAGCAG
1 AAAGACTGGTTTTTCACTCACTAGCAG
652738 A
1 A
652739 GAGGGATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (27 bp):
AAAGACTGGTTTTTCACTCACTAGCAG
Found at i:656287 original size:2 final size:2
Alignment explanation
Indices: 656280--656314 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
656270 ATTTATCAGC
656280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
656315 TTGTTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:668781 original size:46 final size:46
Alignment explanation
Indices: 668709--668847 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
668699 TTTCAAAATA
* *
668709 TTCTTTTCACCCATCATCACTCTTTGACACTCAAATTAGCGTCAAT
1 TTCTTTCCACCCATCATCACTCTTTGACACTAAAATTAGCGTCAAT
* *
668755 TTCTTTCCACCCATCATCACTTTTTGACACTAAAATTAGCATCAAT
1 TTCTTTCCACCCATCATCACTCTTTGACACTAAAATTAGCGTCAAT
* *
668801 TTCTTTCCACCCATCATCACTCTTTGACATTTAAATTAGCGTCAAT
1 TTCTTTCCACCCATCATCACTCTTTGACACTAAAATTAGCGTCAAT
668847 T
1 T
668848 AACTTTTCGT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.38
Consensus pattern (46 bp):
TTCTTTCCACCCATCATCACTCTTTGACACTAAAATTAGCGTCAAT
Found at i:668986 original size:15 final size:17
Alignment explanation
Indices: 668966--669003 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
668956 ACTTATTATT
668966 TTATTTTA-TT-TTTAA
1 TTATTTTAGTTATTTAA
668981 TTATTTTAGTTTATTTAA
1 TTATTTTAG-TTATTTAA
668999 TTATT
1 TTATT
669004 AAAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTATTTTAGTTATTTAA
Found at i:669635 original size:15 final size:15
Alignment explanation
Indices: 669611--669658 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
669601 TTTATTTTTC
669611 TTTTTC-TCTTCTCT
1 TTTTTCTTCTTCTCT
*
669625 TTTTTCTTCTTTTCT
1 TTTTTCTTCTTCTCT
* *
669640 CTTTTCTTCTTCTAT
1 TTTTTCTTCTTCTCT
669655 TTTT
1 TTTT
669659 ATTATAGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCTTCTTCTCT
Found at i:669640 original size:22 final size:20
Alignment explanation
Indices: 669605--669647 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
669595 TATTTATTTA
669605 TTTTTCTTTTTCTCTTCTCT
1 TTTTTCTTTTTCTCTTCTCT
*
669625 TTTTTCTTCTTTTCTCTTTTCT
1 TTTTTC-T-TTTTCTCTTCTCT
669647 T
1 T
669648 CTTCTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTCTTTTTCTCTTCTCT
Found at i:676300 original size:37 final size:37
Alignment explanation
Indices: 676220--676356 Score: 179
Period size: 37 Copynumber: 3.7 Consensus size: 37
676210 ATAATGTTTA
* * * *
676220 CAATGCCTTTTAAGGATCAAGCACAAC-ATCTCAATA
1 CAATGCCTTTTATGGATCAAGCACAACTTTCACAATG
* *
676256 CAATGCCTTCTATGGATTC-AGCACAACTTTCGCAATG
1 CAATGCCTTTTATGGA-TCAAGCACAACTTTCACAATG
*
676293 CAATGCCTTTTATGGATCAAGAACAACTTTCACAATG
1 CAATGCCTTTTATGGATCAAGCACAACTTTCACAATG
*
676330 CAATGCCTTTTATGGATCAAACACAAC
1 CAATGCCTTTTATGGATCAAGCACAAC
676357 CTTTTCTCTC
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
36 24 0.27
37 64 0.73
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (37 bp):
CAATGCCTTTTATGGATCAAGCACAACTTTCACAATG
Found at i:676926 original size:21 final size:21
Alignment explanation
Indices: 676902--676951 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
676892 TGCAAGGGAG
*
676902 GTTTAAAA-CTAATTTAAACAA
1 GTTTAAAAGCT-ATTCAAACAA
676923 GTTTAAAAGCTATTCAAACAA
1 GTTTAAAAGCTATTCAAACAA
*
676944 GTTCAAAA
1 GTTTAAAA
676952 ATCATTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (21 bp):
GTTTAAAAGCTATTCAAACAA
Found at i:677054 original size:21 final size:21
Alignment explanation
Indices: 677024--677081 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
677014 TTGGCACTTC
* *
677024 AAAACTTATTTAAAAAAGTTTA
1 AAAAC-TATTCAAAAAACTTTA
*
677046 AAAACTATTCAAACAACTTTA
1 AAAACTATTCAAAAAACTTTA
*
677067 AAAATTATTCAAAAA
1 AAAACTATTCAAAAA
677082 GTTCAAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAACTATTCAAAAAACTTTA
Found at i:677228 original size:21 final size:20
Alignment explanation
Indices: 677195--677257 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
677185 AAAAACATTT
*
677195 TCAAACAACTTCAAAAATCA
1 TCAAACAAGTTCAAAAATCA
* **
677215 TGCAATCAAGTTCAAGGATCA
1 T-CAAACAAGTTCAAAAATCA
*
677236 CTCAAAGAAGTTCAAAAATCA
1 -TCAAACAAGTTCAAAAATCA
677257 T
1 T
677258 TGAAGCAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.22
Consensus pattern (20 bp):
TCAAACAAGTTCAAAAATCA
Found at i:692076 original size:150 final size:150
Alignment explanation
Indices: 691893--692475 Score: 792
Period size: 150 Copynumber: 3.8 Consensus size: 150
691883 TTTATTGTTA
* * *
691893 TTTTATTTTTTTAATATTAATAATTTATGATTTATTTAAAATATTAATAATTGATAATTTAAATT
1 TTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATA
* * *
691958 TTTATATTTTATTTATAATTTAATCATTAACATTATAAAATATTAATATTTTATTTATAAGTTAA
66 TTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATTTAA
692023 ATGTTATTATGATTATTTAT
131 ATGTTATTATGATTATTTAT
* *
692043 TTTTATTTTTTAAATATGATTAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATA
1 TTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATA
* * * *
692108 TTGATATTTTATTTATAATATAATTATTAATATTTTAAAATATTAATATTTTATTTATAATTTAA
66 TTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATTTAA
*
692173 ATGTTATTATGATTCTTTAT
131 ATGTTATTATGATTATTTAT
** * * * **
692193 TTTTATTTCATTTTAGTTTTTAA-ATATTAATAATTTATTTAAAATAGTAATAATTGATCGTTTA
1 TTTTA-TT--TTTTAAATATTAATA-ATTTATAATTTATTTAAAATATTAATAATTGATAATTTA
692257 AATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAAT
62 AATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAAT
*
692322 TTAAATATTATTATGATTCTTTATTTTTATT
127 TTAAATGTTATTATGA----TTA--TTTA-T
*
692353 TTATAATATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATT-ATTCATTTA
1 TT-T--TATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTGA-TAATTTA
* * *
692417 AATATTAATATTTTATTTTTAATTTAATCATTAATATTTTAAAATATTAATATCTTATT
62 AATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATT
692476 CACAAATATT
Statistics
Matches: 381, Mismatches: 36, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
150 143 0.38
151 2 0.01
152 1 0.00
153 119 0.31
157 2 0.01
159 5 0.01
160 103 0.27
161 2 0.01
162 2 0.01
163 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (150 bp):
TTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAAATA
TTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATTTAA
ATGTTATTATGATTATTTAT
Found at i:692084 original size:27 final size:26
Alignment explanation
Indices: 692047--692103 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
692037 ATTTATTTTT
* *
692047 ATTT-TTTAAATATGATTAATTTATA
1 ATTTATTTAAATATGAATAATTGATA
*
692072 ATTTATTTAAAATATTAATAATTGATA
1 ATTTATTT-AAATATGAATAATTGATA
692099 ATTTA
1 ATTTA
692104 AATATTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 3 0.11
27 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTATTTAAATATGAATAATTGATA
Found at i:692149 original size:42 final size:42
Alignment explanation
Indices: 692073--692172 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
692063 TAATTTATAA
* * *
692073 TTTATTTAAAATATTAATAATTGATAATTTAAATATTGATAT
1 TTTATTTATAATATTAATAATTAATAATTTAAATATTAATAT
* *
692115 TTTATTTATAATA-TAATTATTAATATTTTAAAATATTAATAT
1 TTTATTTATAATATTAATAATTAATAATTT-AAATATTAATAT
692157 TTTATTTATAAT-TTAA
1 TTTATTTATAATATTAA
692173 ATGTTATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 13 0.25
42 38 0.75
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (42 bp):
TTTATTTATAATATTAATAATTAATAATTTAAATATTAATAT
Found at i:692157 original size:22 final size:22
Alignment explanation
Indices: 692050--692157 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 22
692040 TATTTTTATT
* *
692050 TTTTAAATATGATTAATTTATAATT
1 TTTTAAA-AT-ATTAATAT-TAATA
*
692075 TATTTAAAATATTAATAATTGATA
1 T-TTTAAAATATTAAT-ATTAATA
* * *
692099 ATTT-AAATATTGATATT-TTA
1 TTTTAAAATATTAATATTAATA
*
692119 -TTTATAATA-TAATTATTAATA
1 TTTTAAAATATTAA-TATTAATA
692140 TTTTAAAATATTAATATT
1 TTTTAAAATATTAATATT
692158 TTATTTATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
19 5 0.08
20 10 0.15
21 5 0.08
22 21 0.32
23 6 0.09
24 9 0.14
25 4 0.06
26 6 0.09
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
TTTTAAAATATTAATATTAATA
Found at i:692182 original size:48 final size:49
Alignment explanation
Indices: 691983--692182 Score: 110
Period size: 48 Copynumber: 4.0 Consensus size: 49
691973 TAATTTAATC
* * *
691983 ATTAACATTATAAAATATT-AATATTTTATTTATAAGTTAAATGTTATTAT
1 ATTAATATTTTAAAATATTAAATATTTTATTTATAATTTAAATGTTA-T-T
* * ** * * *
692033 GATTATTTATTTTTATTTTTTAAATATGATTAATTTATAATTT--AT-TTAAAAT
1 -ATTA-ATATTTTAAAATATTAAATAT--TTTATTTATAATTTAAATGTT--ATT
* * * * * *
692085 ATTAATAATTGATAAT-TTAAATATTGATATTT-T-ATTTATAATATAATT
1 ATTAATATTTTAAAATATTAAATATT-TTATTTATAATTTA-AATGTTATT
692133 ATTAATATTTTAAAATATT-AATATTTTATTTATAATTTAAATGTTATT
1 ATTAATATTTTAAAATATTAAATATTTTATTTATAATTTAAATGTTATT
692181 AT
1 AT
692183 GATTCTTTAT
Statistics
Matches: 108, Mismatches: 27, Indels: 31
0.65 0.16 0.19
Matches are distributed among these distances:
46 4 0.04
47 7 0.06
48 35 0.32
49 17 0.16
50 6 0.06
51 8 0.07
52 11 0.10
53 7 0.06
54 1 0.01
55 12 0.11
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (49 bp):
ATTAATATTTTAAAATATTAAATATTTTATTTATAATTTAAATGTTATT
Found at i:692290 original size:153 final size:152
Alignment explanation
Indices: 691893--692475 Score: 759
Period size: 153 Copynumber: 3.8 Consensus size: 152
691883 TTTATTGTTA
* * *
691893 TTTTATTT-TTTTAA-TATT-AATAATTTATGATTTATTTAAAATATTAATAATTGATAATTTAA
1 TTTTATTTATTTTAATTTTTAAAT-ATTAATAATTTATTTAAAATATTAATAATTGATAATTTAA
* * * *
691955 ATTTTTATATTTTATTTATAATTTAATCATTAACATTATAAAATATTAATATTTTATTTATAAGT
65 ATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATT
*
692020 TAAATGTTATTATGATTATTTAT
130 TAAATGTTATTATGATTCTTTAT
* *
692043 TTTTATTT-TTTAAATATGATT-AAT-TT-ATAATTTATTTAAAATATTAATAATTGATAATTTA
1 TTTTATTTATTTTAAT-T-TTTAAATATTAATAATTTATTTAAAATATTAATAATTGATAATTTA
* * * *
692104 AATATTGATATTTTATTTATAATATAATTATTAATATTTTAAAATATTAATATTTTATTTATAAT
64 AATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAAT
692169 TTAAATGTTATTATGATTCTTTAT
129 TTAAATGTTATTATGATTCTTTAT
* * **
692193 TTTTATTTCATTTTAGTTTTTAAATATTAATAATTTATTTAAAATAGTAATAATTGATCGTTTAA
1 TTTTATTT-ATTTTAATTTTTAAATATTAATAATTTATTTAAAATATTAATAATTGATAATTTAA
692258 ATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATT
65 ATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATT
*
692323 TAAATATTATTATGATTCTTTAT
130 TAAATGTTATTATGATTCTTTAT
** *
692346 TTTTATTTTATAATATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATT-AT
1 TTTTA-TTTATTTTAATTTTTAAATA-T--T-A---ATAATTTATTTAAAATATTAATAATTGA-
* * * *
692410 TCATTTAAATATTAATATTTTATTTTTAATTTAATCATTAATATTTTAAAATATTAATATCTTAT
57 TAATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTAT
692475 T
122 T
692476 CACAAATATT
Statistics
Matches: 387, Mismatches: 29, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
150 138 0.36
151 6 0.02
152 8 0.02
153 141 0.36
154 4 0.01
156 1 0.00
157 1 0.00
159 1 0.00
160 87 0.22
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (152 bp):
TTTTATTTATTTTAATTTTTAAATATTAATAATTTATTTAAAATATTAATAATTGATAATTTAAA
TATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTATAATTT
AAATGTTATTATGATTCTTTAT
Found at i:692302 original size:42 final size:41
Alignment explanation
Indices: 692256--692475 Score: 174
Period size: 42 Copynumber: 5.4 Consensus size: 41
692246 TTGATCGTTT
692256 AAATATTAATATTTTATTTATAATTTAATCATTAATATTATA
1 AAATATTAATATTTTATTTATAATTTAAT-ATTAATATTATA
*
692298 AAATATTAATATTTTATTTATAATTTAA-A-TATTATTAT-
1 AAATATTAATATTTTATTTATAATTTAATATTAATATTATA
* * * * *
692336 GATTCTTTAT-TTTTATTTTATAATATT--TTTTAAATATTA-A
1 AAATATTAATATTTTA-TTTATAAT-TTAATATT-AATATTATA
* * * *
692376 TAAT-TT-ATAATTTATTTAAAATATTAATAATTATTCATT-T-
1 AAATATTAATATTTTATTTATAAT-TTAAT-ATTAAT-ATTATA
* *
692416 AAATATTAATATTTTATTTTTAATTTAATCATTAATATTTTA
1 AAATATTAATATTTTATTTATAATTTAAT-ATTAATATTATA
*
692458 AAATATTAATATCTTATT
1 AAATATTAATATTTTATT
692476 CACAAATATT
Statistics
Matches: 142, Mismatches: 20, Indels: 32
0.73 0.10 0.16
Matches are distributed among these distances:
37 5 0.04
38 26 0.18
39 17 0.12
40 18 0.13
41 18 0.13
42 58 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (41 bp):
AAATATTAATATTTTATTTATAATTTAATATTAATATTATA
Found at i:692311 original size:111 final size:111
Alignment explanation
Indices: 692100--692316 Score: 249
Period size: 111 Copynumber: 2.0 Consensus size: 111
692090 TAATTGATAA
* * * * *
692100 TTTAAATATTGATATTTTATTTATAATATAATTATTAATATTTTAAAATATTAATATTTTATTTA
1 TTTAAATATTAATAATTTATTTAAAATATAATAATTAATAGTTTAAAATATTAATATTTTATTTA
* * **** **
692165 TAATTTAAATGTTATTATGATTCTTTATTTTTATTTCATTTTAGTT
66 TAATTTAAATATTAATATGATAAAATATTAATATTTCATTTTAGTT
* *
692211 TTTAAATATTAATAATTTATTTAAAATAGTAATAATTGATCGTTT-AAATATTAATATTTTATTT
1 TTTAAATATTAATAATTTATTTAAAATA-TAATAATTAATAGTTTAAAATATTAATATTTTATTT
* *
692275 ATAATTT-AATCATTAATATTATAAAATATTAATATTTTATTT
65 ATAATTTAAAT-ATTAATATGATAAAATATTAATATTTCATTT
692317 ATAATTTAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
110 3 0.03
111 72 0.83
112 12 0.14
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (111 bp):
TTTAAATATTAATAATTTATTTAAAATATAATAATTAATAGTTTAAAATATTAATATTTTATTTA
TAATTTAAATATTAATATGATAAAATATTAATATTTCATTTTAGTT
Found at i:692373 original size:27 final size:27
Alignment explanation
Indices: 692352--692407 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
692342 TTATTTTTAT
*
692352 TTTATAATATT-TTTTAAATATTAATAA
1 TTTATAAT-TTATTTAAAATATTAATAA
692379 TTTATAATTTATTTAAAATATTAATAA
1 TTTATAATTTATTTAAAATATTAATAA
692406 TT
1 TT
692408 ATTCATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTATAATTTATTTAAAATATTAATAA
Found at i:692415 original size:27 final size:26
Alignment explanation
Indices: 692352--692457 Score: 89
Period size: 26 Copynumber: 4.2 Consensus size: 26
692342 TTATTTTTAT
*
692352 TTTATAATATTTTTTAAATATTAATAA
1 TTTATAAT-TTATTTAAATATTAATAA
692379 TTTATAATTTATTTAAAATATTAATAA
1 TTTATAATTTATTT-AAATATTAATAA
* *
692406 --T-T-ATTCATTTAAATATTAATAT
1 TTTATAATTTATTTAAATATTAATAA
* *
692428 TTTAT-TTTTAATTT-AATCATTAATAT
1 TTTATAATTT-ATTTAAAT-ATTAATAA
692454 TTTA
1 TTTA
692458 AAATATTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.16
23 7 0.10
24 2 0.03
25 7 0.10
26 21 0.31
27 20 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTATAATTTATTTAAATATTAATAA
Found at i:692475 original size:21 final size:20
Alignment explanation
Indices: 692204--692489 Score: 84
Period size: 20 Copynumber: 14.0 Consensus size: 20
692194 TTTATTTCAT
*
692204 TTTAGTTTTTAAATATTAATAA
1 TTTA-TTTTAAAATATTAAT-A
*
692226 TTTA-TTTAAAATAGTAATAA
1 TTTATTTTAAAATATTAAT-A
*
692246 TTGATCGTTT-AAATATTAATA
1 TTTAT--TTTAAAATATTAATA
*
692267 TTT-TATTTATAAT-TTAATCA
1 TTTAT-TTTAAAATATTAAT-A
*
692287 TTAATATTATAAAATATTAATA
1 TT--TATTTTAAAATATTAATA
*
692309 TTT-TATTTATAAT-TTAA-A
1 TTTAT-TTTAAAATATTAATA
* * * * * *
692327 TATTATTAT-GATTCTTTATT
1 T-TTATTTTAAAATATTAATA
*
692347 TTTATTTTATAATATT--T-
1 TTTATTTTAAAATATTAATA
*
692364 TTTAAATATTAATAAT-TT-ATAA
1 TTT--ATTTTAA-AATATTAAT-A
692386 TTTA-TTTAAAATATTAATA
1 TTTATTTTAAAATATTAATA
* *
692405 ATTATTCATTTAAATATTAATA
1 TTTATT--TTAAAATATTAATA
*
692427 TTTTATTTT-TAAT-TTAATCA
1 -TTTATTTTAAAATATTAAT-A
692447 TTAATATTTTAAAATATTAATA
1 TT--TATTTTAAAATATTAATA
*
692469 TCTTA-TTCACAAATATTAATA
1 T-TTATTTTA-AAATATTAATA
692490 AGGGTAGGGT
Statistics
Matches: 201, Mismatches: 29, Indels: 69
0.67 0.10 0.23
Matches are distributed among these distances:
17 3 0.01
18 8 0.04
19 50 0.25
20 52 0.26
21 24 0.12
22 44 0.22
23 20 0.10
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTATTTTAAAATATTAATA
Found at i:695799 original size:33 final size:33
Alignment explanation
Indices: 695762--695828 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
695752 AGAAACATTG
695762 TCGTTATCTGACTGAGATACAAGCACATTAATA
1 TCGTTATCTGACTGAGATACAAGCACATTAATA
695795 TCGTTATCTGACTGAGATACAAGCACATTAATA
1 TCGTTATCTGACTGAGATACAAGCACATTAATA
695828 T
1 T
695829 ATATATANNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
TCGTTATCTGACTGAGATACAAGCACATTAATA
Found at i:698422 original size:21 final size:19
Alignment explanation
Indices: 698376--698413 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
698366 TAAAACAACT
*
698376 AGAAAGTATTTAAAAAGAG
1 AGAAAATATTTAAAAAGAG
698395 AGAAAATATTTAAAAAGAG
1 AGAAAATATTTAAAAAGAG
698414 TAAGAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (19 bp):
AGAAAATATTTAAAAAGAG
Found at i:707491 original size:29 final size:29
Alignment explanation
Indices: 707444--707513 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
707434 TCTCTTGATT
707444 GAAGATGAAGAAGATGACATGCAAAGAGAC
1 GAAGATGAA-AAGATGACATGCAAAGAGAC
* **
707474 GAAGATGAAAAGATGACATGGAAAGAGGT
1 GAAGATGAAAAGATGACATGCAAAGAGAC
707503 GAAGATGAAAA
1 GAAGATGAAAA
707514 AGAAGAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.51, C:0.06, G:0.31, T:0.11
Consensus pattern (29 bp):
GAAGATGAAAAGATGACATGCAAAGAGAC
Found at i:711980 original size:18 final size:18
Alignment explanation
Indices: 711939--711977 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
711929 ATATTGTTAC
711939 AAAATTATGAGACCAATG
1 AAAATTATGAGACCAATG
* *
711957 AAAATTTTGAG-CCTATG
1 AAAATTATGAGACCAATG
711974 AAAA
1 AAAA
711978 ATTAAGACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (18 bp):
AAAATTATGAGACCAATG
Found at i:713512 original size:68 final size:68
Alignment explanation
Indices: 713429--713627 Score: 202
Period size: 68 Copynumber: 2.9 Consensus size: 68
713419 GTTGTTTTTT
* * **
713429 TTTCACATACTATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTACATGTTGT
1 TTTCACATACTATATGAGATAACAATGAGCACATGATGTATGCTATGTTGCAATGTACATGATAA
*
713494 TG-
66 GGA
* * * * * **
713496 TTTCCACATACTATATGGGATGACAATGAGTACATGATGTGTGCTATGTTGAAATGTATGTGATA
1 TTT-CACATACTATATGAGATAACAATGAGCACATGATGTATGCTATGTTGCAATGTACATGATA
713561 AGGA
65 AGGA
* * * * * * * *
713565 TTTCGCATACCATATTAGATAATAATGAGCACATGAGGTATGCGATGCTGCAATGTATATGAT
1 TTTCACATACTATATGAGATAACAATGAGCACATGATGTATGCTATGTTGCAATGTACATGAT
713628 GACGATTCCA
Statistics
Matches: 105, Mismatches: 25, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
67 3 0.03
68 99 0.94
69 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (68 bp):
TTTCACATACTATATGAGATAACAATGAGCACATGATGTATGCTATGTTGCAATGTACATGATAA
GGA
Found at i:719289 original size:65 final size:65
Alignment explanation
Indices: 719195--719386 Score: 222
Period size: 65 Copynumber: 2.9 Consensus size: 65
719185 GTTGCAATGT
*
719195 ATATTATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGTGATGTTTCCAC
1 ATATTATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGTGATGATTCCAC
* ** * * *
719260 ATATTATATGAGATAAGAATAAGTTCATGATGTGTGCTACGTTGCAATGTATGCGATGAGGATTC
1 ATATTATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTAT--G-TGATGATTC
***
719325 TGT
63 CAC
** * * *
719328 ATACCATATGAGATAATAATGAGCACATGATGCATGCTATGTTGTAATGTATGTGATGA
1 ATATTATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGTGATGA
719387 AGATTCCACA
Statistics
Matches: 103, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
65 52 0.50
66 1 0.01
67 1 0.01
68 49 0.48
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (65 bp):
ATATTATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGTGATGATTCCAC
Found at i:719366 original size:68 final size:67
Alignment explanation
Indices: 719200--719411 Score: 221
Period size: 68 Copynumber: 3.2 Consensus size: 67
719190 AATGTATATT
* *
719200 ATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTAT-G-TGATGTTTCCACATA
1 ATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGGATGAAGATTCCACATA
**
719263 TT
66 CC
* ** * * * ***
719265 ATATGAGATAAGAATAAGTTCATGATGTGTGCTACGTTGCAATGTATGCGATGAGGATTCTGTAT
1 ATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATG-GATGAAGATTCCACAT
719330 ACC
65 ACC
* * *
719333 ATATGAGATAATAATGAGCACATGATGCATGCTATGTTGTAATGTATGTGATGAAGATTCCACAT
1 ATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATG-GATGAAGATTCCACAT
* *
719398 GCT
65 ACC
*
719401 TTATGAGATAA
1 ATATGAGATAA
719412 ATATGAGTGA
Statistics
Matches: 116, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
65 42 0.36
67 1 0.01
68 73 0.63
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (67 bp):
ATATGAGATAAGAATGAGCACATGATGTATGCTATGTTGCAATGTATGGATGAAGATTCCACATA
CC
Found at i:726423 original size:59 final size:57
Alignment explanation
Indices: 726353--726474 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 57
726343 CAATCTCTTG
726353 ATTTTGGCCAAAG-TGTTGAGAAAAT-TAAGAAAGGTTTTCTTTCATTCTAAAATTTTTGA
1 ATTTTGGCCAAAGCT-TTGAGAAAATATAA-AAA-GTTTTC-TTCATTCTAAAATTTTTGA
* * * * *
726412 ATTTTTGCCAAAGCTTTGGGAAAGTCATAAAAAGTTTTCTTCATTTTAACATTTTTGA
1 ATTTTGGCCAAAGCTTTGAGAAAAT-ATAAAAAGTTTTCTTCATTCTAAAATTTTTGA
726470 ATTTT
1 ATTTT
726475 CAGCAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
58 22 0.40
59 26 0.47
60 4 0.07
61 3 0.05
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (57 bp):
ATTTTGGCCAAAGCTTTGAGAAAATATAAAAAGTTTTCTTCATTCTAAAATTTTTGA
Found at i:750334 original size:384 final size:381
Alignment explanation
Indices: 749268--750415 Score: 1699
Period size: 384 Copynumber: 3.0 Consensus size: 381
749258 TAAGATAAAG
* *
749268 ACATGAAGGTAGTTGAAGCTTGGGATGATGGATATTGGGATATCCTTTTTTGATGCCATTTATTT
1 ACATGAAGGTAGTCGAAGCTTGGGATGATGGATATTGGGATATCCTTTTTTGATGACATTTATTT
* *
749333 GCATGGGAAGAGACAATCCTCTGAGATTGGTTGTCAAAATTGGAAGATATGATTATTGTGTAAGA
66 GCATGGGAAGAGACAATCCTCCGAGATTGGTTGTCAAAATTGGAAGATATGATTATTGTGCAAGA
* * * ** *
749398 TAGGATAGATAAATTGTTTTGGATTAATGACCCTCAATGAGGCTTATCAATCAAAAGATTTGTAT
131 TAGGATAGATAGATTGATTTGGATTAATGACCCTAAATGAGGCTTATCGGTTAAAAGATTTGTAT
* ** * *
749463 TAATTATGGACTCCTCTTTTAATGAGGGTAGTCGAAAGGTATGATTTTTCTCCTTTTGGAAATTA
196 CAACCATGGACTCCTCTCTTAATGAGGGTAGTC-AAAGGTATGATTTTTCTCCCTTTGGAAATTA
* * *
749528 AATGTTCCACTTAATGTCCAATTTTTTTTTATGGATGGCTATTTTTGATAATACTCCTACTAGAG
260 AATGTTCCACTTAAAGTCCAA-TGTTTTTTATGGATGGCTATTTTTTAT-ATACTCCTACTAGAG
* * *
749593 GTTTTTTGAGATATAGAGGAATCCATATGGATAATAATTCTTGTTTGTGTGCATGGTGT
323 GTTTTTTGAGATATAGAGGAATCCATGTGGATAATAATTCTTGCTTGTGTGCATGGTGC
* * * **
749652 ATATGAAGGTAGTCAAAGCTTGGGCTGATGGATATTAAGATATCCTTTTTTGAT-ACCATTTATT
1 ACATGAAGGTAGTCGAAGCTTGGGATGATGGATATTGGGATATCCTTTTTTGATGA-CATTTATT
* * *
749716 TGCATGGGAGGAGAAAATCCTCCGAGATTGGTTGTCAAAATTGGAAGATATGATTATTGTAC-A-
65 TGCATGGGAAGAGACAATCCTCCGAGATTGGTTGTCAAAATTGGAAGATATGATTATTGTGCAAG
* * *
749779 ATAGGATAGATAGATTAATTTGGATTAATGACCCTAAATGAGGGTTATCGGTTAAAATATTTGTA
130 ATAGGATAGATAGATTGATTTGGATTAATGACCCTAAATGAGGCTTATCGGTTAAAAGATTTGTA
* *
749844 TCAACCATGGACTCCTTTCTTAATGAGGGTAGTTAAAAGGTATGATTTTTCTCCCTTTGGAAATT
195 TCAACCATGGACTCCTCTCTTAATGAGGGTAG-TCAAAGGTATGATTTTTCTCCCTTTGGAAATT
* *
749909 AAATGTTTCACTTAAAGTCCAATGTTTTTTATGGATGGCTATTTTTTATGATACTCCTACCAGAG
259 AAATGTTCCACTTAAAGTCCAATGTTTTTTATGGATGGCTATTTTTTAT-ATACTCCTACTAGAG
*
749974 GTTTTTTGAGATATAGAGGAATCCATGTGGATAATAATTCTTACTTGTGTGCATGGTGC
323 GTTTTTTGAGATATAGAGGAATCCATGTGGATAATAATTCTTGCTTGTGTGCATGGTGC
* * * ** *
750033 ACATGAAGGTAGTCGAACCTTGGGATGAAGGATATTGGGATATCATTTTTCAATGACATCTATTT
1 ACATGAAGGTAGTCGAAGCTTGGGATGATGGATATTGGGATATCCTTTTTTGATGACATTTATTT
* *
750098 GCATGGGAAGAGACAATCCTCCAAGATTGGTTGTCAAAAATTGGAAGACATGATTATTGTGCAAG
66 GCATGGGAAGAGACAATCCTCCGAGATTGGTTGTC-AAAATTGGAAGATATGATTATTGTGCAAG
* * *
750163 ATAGGATAGATAGATTGATTTGGATTAATGGCCCTAAAGGAGCCTTATCGGTTAAAAGATTTGTA
130 ATAGGATAGATAGATTGATTTGGATTAATGACCCTAAATGAGGCTTATCGGTTAAAAGATTTGTA
* *
750228 TCAACCATGGACTTCTCTCTTAATGAGAGTAGTCAAATGGTATGATTTTTCTCCCTTTGGAAATT
195 TCAACCATGGACTCCTCTCTTAATGAGGGTAGTCAAA-GGTATGATTTTTCTCCCTTTGGAAATT
*
750293 AAATGTTCCACTTAAAGTCCAATGTTTTTTATGGATGGCTATTTTTTATAGTACTCTTACTAGAG
259 AAATGTTCCACTTAAAGTCCAATGTTTTTTATGGATGGCTATTTTTTATA-TACTCCTACTAGAG
* * * *
750358 GTTTTTTGAGATTTAGAGGGATCCATGAGGATAATAATTCTTGCTTGTGGGCATGGTG
323 GTTTTTTGAGATATAGAGGAATCCATGTGGATAATAATTCTTGCTTGTGTGCATGGTG
750416 TCCTTTGGCG
Statistics
Matches: 684, Mismatches: 72, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
381 178 0.26
382 157 0.23
383 8 0.01
384 341 0.50
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (381 bp):
ACATGAAGGTAGTCGAAGCTTGGGATGATGGATATTGGGATATCCTTTTTTGATGACATTTATTT
GCATGGGAAGAGACAATCCTCCGAGATTGGTTGTCAAAATTGGAAGATATGATTATTGTGCAAGA
TAGGATAGATAGATTGATTTGGATTAATGACCCTAAATGAGGCTTATCGGTTAAAAGATTTGTAT
CAACCATGGACTCCTCTCTTAATGAGGGTAGTCAAAGGTATGATTTTTCTCCCTTTGGAAATTAA
ATGTTCCACTTAAAGTCCAATGTTTTTTATGGATGGCTATTTTTTATATACTCCTACTAGAGGTT
TTTTGAGATATAGAGGAATCCATGTGGATAATAATTCTTGCTTGTGTGCATGGTGC
Found at i:758297 original size:62 final size:62
Alignment explanation
Indices: 758200--758321 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
758190 GATTTATGTG
* * * *
758200 TCTTGCAACATATATTAATATGGAGCAAGTGTCCATTTTTAATACTAATGGATCCTAGATTT
1 TCTTGCAACATATATTAATATGGAGCAACTATCCATTTTCAATACTAATGGATCCAAGATTT
* * * *
758262 TCTTGCAACATATATTAATTTAGG-GTAACTATCCATTTTCAGTATTAATGGATCCAAGAT
1 TCTTGCAACATATATTAATAT-GGAGCAACTATCCATTTTCAATACTAATGGATCCAAGAT
758322 GAATTAAGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 49 0.96
63 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (62 bp):
TCTTGCAACATATATTAATATGGAGCAACTATCCATTTTCAATACTAATGGATCCAAGATTT
Found at i:760951 original size:93 final size:93
Alignment explanation
Indices: 760792--761070 Score: 517
Period size: 93 Copynumber: 3.0 Consensus size: 93
760782 AGAGCTCGTT
*
760792 AGTCACCTGAGTCATGGAGAT-TGGATTCGTCCTTCTTTCTTGGTAAGTGTATAGCAACCTTTTT
1 AGTCACCTGAGTCATGGAGATGT-GATTCGTCCTTCTTTCTTGGTAAGTGTATAGCAACCTTCTT
760856 GAAACCTAAAGAATTGTGTCATGTATCAC
65 GAAACCTAAAGAATTGTGTCATGTATCAC
760885 AGTCACCTGAGTCATGGAGATGTGATTCGTCCTTCTTTCTTGGTAAGTGTATAGCAACCTTCTTG
1 AGTCACCTGAGTCATGGAGATGTGATTCGTCCTTCTTTCTTGGTAAGTGTATAGCAACCTTCTTG
760950 AAACCTAAAGAATTGTGTCATGTATCAC
66 AAACCTAAAGAATTGTGTCATGTATCAC
760978 AGTCACCTGAGTCATTGGAGATGTGATTCGTCCTTCTTTCTT-GTAAGTGTATAGCAACCTTCTT
1 AGTCACCTGAGTCA-TGGAGATGTGATTCGTCCTTCTTTCTTGGTAAGTGTATAGCAACCTTCTT
761042 GAAACCTAAAGAATTGTGTCATGTATCAC
65 GAAACCTAAAGAATTGTGTCATGTATCAC
761071 TTGATGAGTC
Statistics
Matches: 183, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
93 155 0.85
94 28 0.15
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (93 bp):
AGTCACCTGAGTCATGGAGATGTGATTCGTCCTTCTTTCTTGGTAAGTGTATAGCAACCTTCTTG
AAACCTAAAGAATTGTGTCATGTATCAC
Found at i:768772 original size:31 final size:31
Alignment explanation
Indices: 768732--768855 Score: 149
Period size: 31 Copynumber: 4.0 Consensus size: 31
768722 ATTAGTTTCT
* *
768732 CAACTTTTTTTTTGTTTTTCAATTTAATCCTC
1 CAAC-TTTTTTCTCTTTTTCAATTTAATCCTC
* * * *
768764 CAACTTTTTTCTCTTTGTCAATTTAGTCTTT
1 CAACTTTTTTCTCTTTTTCAATTTAATCCTC
* *
768795 CAATTTTTTTCTCTTTTTAAATTTAATCCTC
1 CAACTTTTTTCTCTTTTTCAATTTAATCCTC
* *
768826 TAACATTTTTCTCTTTTTCAATTTAATCCT
1 CAACTTTTTTCTCTTTTTCAATTTAATCCT
768856 TATTCCATGC
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
31 72 0.95
32 4 0.05
ACGTcount: A:0.20, C:0.19, G:0.02, T:0.58
Consensus pattern (31 bp):
CAACTTTTTTCTCTTTTTCAATTTAATCCTC
Found at i:768818 original size:62 final size:63
Alignment explanation
Indices: 768719--768850 Score: 180
Period size: 62 Copynumber: 2.1 Consensus size: 63
768709 TGCCTTATTT
* * * *
768719 TCAA-TTAGTTTCTCAACTTTTTTTTTGTTTTTCAATTTAATCCTCCAACTTTTTTCTCTTTG
1 TCAATTTAGTTTCTCAACTTTTTTTCTCTTTTTAAATTTAATCCTCCAACATTTTTCTCTTTG
* *
768781 TCAATTTAGTCTT-TCAA-TTTTTTTCTCTTTTTAAATTTAATCCTCTAACATTTTTCTCTTTT
1 TCAATTTAGT-TTCTCAACTTTTTTTCTCTTTTTAAATTTAATCCTCCAACATTTTTCTCTTTG
768843 TCAATTTA
1 TCAATTTA
768851 ATCCTTATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 51 0.82
63 9 0.15
64 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.58
Consensus pattern (63 bp):
TCAATTTAGTTTCTCAACTTTTTTTCTCTTTTTAAATTTAATCCTCCAACATTTTTCTCTTTG
Found at i:771553 original size:2 final size:2
Alignment explanation
Indices: 771546--771573 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
771536 TAGTGTCAGA
771546 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
771574 TACCTGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:775805 original size:20 final size:19
Alignment explanation
Indices: 775780--775822 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
775770 CTCTTAAAGT
775780 AATTTAAAATAAAATACTTA
1 AATTT-AAATAAAATACTTA
*
775800 AATTTAACTAAAATACTTA
1 AATTTAAATAAAATACTTA
775819 AATT
1 AATT
775823 AATCACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTTAAATAAAATACTTA
Found at i:776341 original size:2 final size:2
Alignment explanation
Indices: 776334--776367 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
776324 GTCTTCAATA
776334 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
776368 TACAGGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:776354 original size:15 final size:15
Alignment explanation
Indices: 776334--776367 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
776324 GTCTTCAATA
776334 ATATATATATATATT
1 ATATATATATATATT
776349 ATATATATATATATT
1 ATATATATATATATT
776364 ATAT
1 ATAT
776368 TACAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:776367 original size:13 final size:13
Alignment explanation
Indices: 776335--776360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
776325 TCTTCAATAA
776335 TATATATATATAT
1 TATATATATATAT
776348 TATATATATATAT
1 TATATATATATAT
776361 ATTATATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:777548 original size:122 final size:122
Alignment explanation
Indices: 777329--777573 Score: 427
Period size: 122 Copynumber: 2.0 Consensus size: 122
777319 CAAGGCCAAT
*
777329 TTTTTAAATGAGAAACCCCTTTTCCCTTATAGCCAAGTAATCTTCAAAAAGGCTAACAAATCTCT
1 TTTTTAAATGAGAAACCCCTTTTCCCTTATAGCCAAGTAACCTTCAAAAAGGCTAACAAATCTCT
* *
777394 ATATATATTTACTCCATTCATTTATTCTTTCAAGCCGTTGCATGTAAATTCCATCAA
66 ATATATATTTACTCCATTCATTTATTCATTCAAGCCGCTGCATGTAAATTCCATCAA
*
777451 TTTTTAAATGAGAAACCCCTTTTCCCTTATAGCCAAGTAACCTTCAAAAAGGCTACCAAATCTCT
1 TTTTTAAATGAGAAACCCCTTTTCCCTTATAGCCAAGTAACCTTCAAAAAGGCTAACAAATCTCT
** *
777516 ATATATATTTACTCCATTCATTTATTCATTCAAGGGGCTGCATGTAAATTGCATCAA
66 ATATATATTTACTCCATTCATTTATTCATTCAAGCCGCTGCATGTAAATTCCATCAA
777573 T
1 T
777574 CTATGCATCT
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (122 bp):
TTTTTAAATGAGAAACCCCTTTTCCCTTATAGCCAAGTAACCTTCAAAAAGGCTAACAAATCTCT
ATATATATTTACTCCATTCATTTATTCATTCAAGCCGCTGCATGTAAATTCCATCAA
Found at i:779254 original size:21 final size:19
Alignment explanation
Indices: 779216--779254 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
779206 TTTTGATTTT
*
779216 TTTGATTTATTTTTTTAAC
1 TTTGATTTATTATTTTAAC
779235 TTTGACTTTAATTATTTTAA
1 TTTGA-TTT-ATTATTTTAA
779255 ATATTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTGATTTATTATTTTAAC
Found at i:780669 original size:6 final size:6
Alignment explanation
Indices: 780652--780693 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
780642 TAAAAGGACA
* * *
780652 AAAGAG -AAGAG AAAGAG AAAAAG AAAAAG AAAAAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
780694 TAGAAAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:780702 original size:14 final size:12
Alignment explanation
Indices: 780652--780693 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
780642 TAAAAGGACA
*
780652 AAAGAG-AAGAG
1 AAAGAGAAAAAG
780663 AAAGAGAAAAAG
1 AAAGAGAAAAAG
*
780675 AAAAAGAAAAAG
1 AAAGAGAAAAAG
780687 AAAGAGA
1 AAAGAGA
780694 TAGAAAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 6 0.22
12 21 0.78
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAAG
Found at i:781606 original size:2 final size:2
Alignment explanation
Indices: 781599--781637 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
781589 TGCAGTGTAA
781599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
781638 AAGAGAGATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:784607 original size:29 final size:28
Alignment explanation
Indices: 784539--784605 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
784529 TTAAATTAAA
*
784539 TTAAAATTTTAATTATAAAAAATGATAT
1 TTAAAATTTTAATTATAAAAAATAATAT
* *
784567 TTAAAATTTTAATTATAAATTATTAATATT
1 TTAAAATTTTAATTATAAA-AAATAATA-T
784597 TTAAAATTT
1 TTAAAATTT
784606 AAAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 19 0.56
29 5 0.15
30 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TTAAAATTTTAATTATAAAAAATAATAT
Found at i:784624 original size:29 final size:29
Alignment explanation
Indices: 784539--784624 Score: 70
Period size: 30 Copynumber: 3.0 Consensus size: 29
784529 TTAAATTAAA
** *
784539 TTAAAATTTTAATTATAAAA-AATGATA-T
1 TTAAAA-TTTAAAAATAAAATAATTATATT
* * *
784567 TTAAAATTT-TAATTATAAATTATTAATATT
1 TTAAAATTTAAAAATA-AAATAATT-ATATT
784597 TTAAAATTTAAAAATAAAATAATTATAT
1 TTAAAATTTAAAAATAAAATAATTATAT
784625 ATTGTAATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
26 2 0.05
27 6 0.14
28 8 0.18
29 7 0.16
30 17 0.39
31 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
TTAAAATTTAAAAATAAAATAATTATATT
Found at i:787277 original size:21 final size:21
Alignment explanation
Indices: 787247--787320 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
787237 ATTCATGTAA
*
787247 TTCATGACAAAGACAGATGCC
1 TTCATGACAAAGACAAATGCC
*
787268 TTCGTGACAAAGACAAATGCC
1 TTCATGACAAAGACAAATGCC
* *
787289 TTCATGACAAAGGCAAGTGCC
1 TTCATGACAAAGACAAATGCC
*
787310 TTTATGACAAA
1 TTCATGACAAA
787321 AATTGATGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
TTCATGACAAAGACAAATGCC
Found at i:789270 original size:3 final size:3
Alignment explanation
Indices: 789262--789290 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
789252 ACTTTATCTT
789262 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
789291 ACTTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:791000 original size:2 final size:2
Alignment explanation
Indices: 790993--791022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
790983 NNNNNNNATA
790993 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
791023 AATCTATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:803225 original size:40 final size:40
Alignment explanation
Indices: 803181--803282 Score: 159
Period size: 40 Copynumber: 2.5 Consensus size: 40
803171 TAATCATCTT
* *
803181 TGGTACAAATATATGATTCAGTATGCTGTTTTATTAAGTA
1 TGGTACAGATATATGATTCAGTATGCTGTCTTATTAAGTA
*
803221 TGGTACAGATATATGATTCAGTATGCTGTCTTATTAAGTG
1 TGGTACAGATATATGATTCAGTATGCTGTCTTATTAAGTA
* *
803261 TGGTGCAGATACATGATTCAGT
1 TGGTACAGATATATGATTCAGT
803283 GTTTCTCCCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (40 bp):
TGGTACAGATATATGATTCAGTATGCTGTCTTATTAAGTA
Found at i:803903 original size:6 final size:6
Alignment explanation
Indices: 803892--803922 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
803882 AGCAGCGGCT
803892 GCAGGG GCAGGG GCAGGG GCAGGG GCAGGG G
1 GCAGGG GCAGGG GCAGGG GCAGGG GCAGGG G
803923 GGGCTCACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.68, T:0.00
Consensus pattern (6 bp):
GCAGGG
Found at i:817145 original size:17 final size:17
Alignment explanation
Indices: 817125--817163 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
817115 AAAAATGATG
*
817125 TTCTTATGGAAAT-TATT
1 TTCTTACGGAAATCT-TT
817142 TTCTTACGGAAATCTTT
1 TTCTTACGGAAATCTTT
817159 TTCTT
1 TTCTT
817164 TCTTAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (17 bp):
TTCTTACGGAAATCTTT
Found at i:826375 original size:72 final size:72
Alignment explanation
Indices: 826257--826400 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
826247 CTTATTCTTT
826257 AACAAGCACCCATATGTTATCCTCAAGTATCCCATATATTTCAATCTATGAGATCAATTACTTAC
1 AACAAGCACCCATATGTTATCCTCAAGTATCCCATATATTTCAATCTATGAGATCAATTACTTAC
826322 TTTCCAA
66 TTTCCAA
* *
826329 AACAAGCACCCATATGTTATCTTCAAGTATCCCATATACTTT-AATCTATGAGATCGATTACTTA
1 AACAAGCACCCATATGTTATCCTCAAGTATCCCATATA-TTTCAATCTATGAGATCAATTACTTA
826393 CTTTCCAA
65 CTTTCCAA
826401 GTAAAGAGGC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 66 0.96
73 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (72 bp):
AACAAGCACCCATATGTTATCCTCAAGTATCCCATATATTTCAATCTATGAGATCAATTACTTAC
TTTCCAA
Found at i:828888 original size:17 final size:17
Alignment explanation
Indices: 828866--828898 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
828856 AAAATTGTTT
828866 TTCTT-CTTCCATTAAAA
1 TTCTTCCTT-CATTAAAA
828883 TTCTTCCTTCATTAAA
1 TTCTTCCTTCATTAAA
828899 CACTTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (17 bp):
TTCTTCCTTCATTAAAA
Found at i:833191 original size:21 final size:20
Alignment explanation
Indices: 833153--833191 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
833143 CAGAGCTTAG
*
833153 AGGGTCACTATAGTTTTGTC
1 AGGGTCACTATAGCTTTGTC
*
833173 AGGGTCAACTATGGCTTTG
1 AGGGTC-ACTATAGCTTTG
833192 AAAAATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (20 bp):
AGGGTCACTATAGCTTTGTC
Found at i:836479 original size:22 final size:22
Alignment explanation
Indices: 836449--836497 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
836439 TTGAAACTAC
*
836449 ATGTGTGTATCTATATATATAT
1 ATGTATGTATCTATATATATAT
* *
836471 ATGTATGTATGTATATGTATAT
1 ATGTATGTATCTATATATATAT
*
836493 GTGTA
1 ATGTA
836498 CATAGTTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (22 bp):
ATGTATGTATCTATATATATAT
Found at i:849486 original size:18 final size:19
Alignment explanation
Indices: 849460--849502 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
849450 GAGATAGATG
*
849460 AAAAAAATATTTTA-CAAT
1 AAAATAATATTTTATCAAT
*
849478 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATCAAT
849497 AAAATA
1 AAAATA
849503 TTAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATATTTTATCAAT
Found at i:850742 original size:21 final size:21
Alignment explanation
Indices: 850718--850790 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
850708 ATTAATCCTA
*
850718 GAACTTGTTTGAATGATATTT
1 GAACTTGTTTGAATGATTTTT
*
850739 GAACTTGTTTAAATGATTTTT
1 GAACTTGTTTGAATGATTTTT
* **
850760 GAAGTTACTTGAATGAGTTTTT
1 GAACTTGTTTGAATGA-TTTTT
850782 GAACTTGTT
1 GAACTTGTT
850791 CAAATAGTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 31 0.74
22 11 0.26
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.48
Consensus pattern (21 bp):
GAACTTGTTTGAATGATTTTT
Found at i:850799 original size:21 final size:20
Alignment explanation
Indices: 850736--850802 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
850726 TTGAATGATA
850736 TTTGAACTTGTTTAAAT-GATT
1 TTTGAACTTG-TTAAATAG-TT
* * *
850757 TTTGAAGTTACTTGAATGAGTT
1 TTTGAACTT-GTTAAAT-AGTT
850779 TTTGAACTTGTTCAAATAGTT
1 TTTGAACTTGTT-AAATAGTT
850800 TTT
1 TTT
850803 AAATGTGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 22 0.61
22 13 0.36
23 1 0.03
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTGAACTTGTTAAATAGTT
Found at i:864543 original size:24 final size:24
Alignment explanation
Indices: 864498--864543 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
864488 TTCTCAAACA
**
864498 TCATCAAGCATCATTTAGCATTTT
1 TCATCAAGCATCATCCAGCATTTT
* *
864522 TCATCAAGCATTATCCATCATT
1 TCATCAAGCATCATCCAGCATT
864544 GAGCATCATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (24 bp):
TCATCAAGCATCATCCAGCATTTT
Found at i:868504 original size:2 final size:2
Alignment explanation
Indices: 868497--868535 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
868487 TTTTTCACCA
*
868497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
868536 ATTAACTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:877299 original size:12 final size:12
Alignment explanation
Indices: 877282--877306 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
877272 ATTAATGGAT
877282 TATTGAACTCTG
1 TATTGAACTCTG
877294 TATTGAACTCTG
1 TATTGAACTCTG
877306 T
1 T
877307 TTTATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TATTGAACTCTG
Found at i:878036 original size:44 final size:44
Alignment explanation
Indices: 877884--878038 Score: 131
Period size: 44 Copynumber: 3.5 Consensus size: 44
877874 TTATAAAAAG
* * * **
877884 TAAAATATATTTATATTATTTGAGCTATGATGCAAACTTAAATACG
1 TAAAA-AT-TTTATATTAGTTGAACTATTATGCAAACTTAAATATA
* * * *
877930 T-AAAATTTTATATTAGTTGAACTTATTA-AC-TAC-GAAATGTA
1 TAAAAATTTTATATTAGTTGAAC-TATTATGCAAACTTAAATATA
* *
877971 -AAATAAATTTATATTATTTGAACTATTATGCAAACTTAAATATA
1 TAAA-AATTTTATATTAGTTGAACTATTATGCAAACTTAAATATA
*
878015 TAAAAATTTTCTATTAGTTGAACT
1 TAAAAATTTTATATTAGTTGAACT
878039 TTTGAAGTAA
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
41 11 0.13
42 20 0.24
43 17 0.20
44 29 0.35
45 6 0.07
46 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (44 bp):
TAAAAATTTTATATTAGTTGAACTATTATGCAAACTTAAATATA
Found at i:878065 original size:86 final size:85
Alignment explanation
Indices: 877883--878072 Score: 247
Period size: 86 Copynumber: 2.2 Consensus size: 85
877873 ATTATAAAAA
* * * *
877883 GTAAAATATATTTATATTATTTGAGCTATGATGCAAACTTAAATACGTAAAATTTTATATTAGTT
1 GTAAAACAAATTTATATTATTTGAACTATGATGCAAACTTAAATACATAAAATTTTATATTAGTT
*
877948 GAACTTATTAACTACGAAAT
66 GAACTTATTAACTAAGAAAT
* * * *
877968 GTAAAATAAATTTATATTATTTGAACTATTATGCAAACTTAAATATATAAAAATTTTCTATTAGT
1 GTAAAACAAATTTATATTATTTGAACTATGATGCAAACTTAAATACAT-AAAATTTTATATTAGT
* *
878033 TGAACTT-TTGAAGTAATAAAT
65 TGAACTTATT-AACTAAGAAAT
*
878054 GTAAAGCAAATTTATATTA
1 GTAAAACAAATTTATATTA
878073 CTCGAATATA
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 45 0.49
86 47 0.51
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (85 bp):
GTAAAACAAATTTATATTATTTGAACTATGATGCAAACTTAAATACATAAAATTTTATATTAGTT
GAACTTATTAACTAAGAAAT
Found at i:886044 original size:25 final size:25
Alignment explanation
Indices: 885994--886063 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
885984 CTAAGCCGAA
*
885994 CCTTCCTTTCCTTT-TTCTTCTTCCT
1 CCTTCCTTT-CTTTCTTCTTCTCCCT
886019 CCTTCCTTTCTTTCTTCCTT-TCCCT
1 CCTTCCTTTCTTTCTT-CTTCTCCCT
* *
886044 -CTTTCTTCCTTTC-TCTTCTC
1 CCTTCCTTTCTTTCTTCTTCTC
886064 ACTTTGTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.08
23 3 0.08
24 15 0.38
25 15 0.38
26 3 0.08
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (25 bp):
CCTTCCTTTCTTTCTTCTTCTCCCT
Found at i:894953 original size:467 final size:462
Alignment explanation
Indices: 894068--894982 Score: 1715
Period size: 467 Copynumber: 2.0 Consensus size: 462
894058 GTTGCAACTT
894068 TTGAGTAAAAGAGTTTTTTAGATTCTTTTCAAACCATTTTGCTAATTTGTTGATTATCAGAATCA
1 TTGAGTAAAAGAGTTTTTTAGATTCTTTTCAAACCATTTTGCTAATTTGTTGATTATCAGAATCA
894133 TTTGAATTTGTTTGTTGATTTACCATATCTATTGAATGAGTTTGCTATGTTGGCGTTTCAAGGAC
66 TTTGAATTTGTTTGTTGATTTACCATATCTATTGAATGAGTTTGCTATGTTGGCGTTTCAAGGAC
894198 TACTATTCTTGAGTTTTAACTTTCTAAAGCATCAATGCGATTTTGAATCTCTTCAAAAATGATTT
131 TACTATTCTTGAGTTTTAACTTTCTAAAGCATCAATGCGATTTTGAATCTCTTCAAAAATGATTT
894263 TGAATGATTATGCACAAATGGCCAAGTACAAGCCATAAATGTGATAAATTCCATCCAATCACACA
196 TGAATGATTATGCACAAATGGCCAAGTACAAGCCATAAATGTGATAAATTCCATCCAATCACACA
*
894328 TTGTCCATGCATGTGAACAGTAAAAGCCAGGCTAAAATTTGAGTAAAATAAAGTTAAAAAATTAT
261 TTGTCCAGGCATGTGAACAGTAAAAGCCAGGCTAAAATTTGAGTAAAATAAAGTTAAAAAATTAT
*
894393 CAAGAAAAATGATGATGGTTCAGCTAGGATCAGCCCACAGAGCCATTTTGGATCCAAGCGGCACC
326 CAAGAAAAATGATGATGGTTCAGCTAAGATCAGCCCACAGAGCCATTTTGGATCCAAGCGGCACC
*
894458 AGTCTGTTATCCTTCCACTGCAAAGAGCGGGAAGTCTTCGCTGCTTTGTGAATCCAGCCTCACGC
391 AGCCTGTTATCCTTCCACTGCAAAGAGCGGGAAGTCTT--CT-C--TGTGAATCCAGCCTCACGC
894523 GGTGCCCTCCAC
451 GGTGCCCTCCAC
*
894535 TTGAGTAAAAGAGTTTTTTAGATTCTTTTCAAACCATTTTGCTAATTTGTTGATTATCAGAATCG
1 TTGAGTAAAAGAGTTTTTTAGATTCTTTTCAAACCATTTTGCTAATTTGTTGATTATCAGAATCA
894600 TTTGAATTTGTTTGTTGATTTACCATATCTATTGAATGAGTTTGCTATGTTGGCGTTTCAAGGAC
66 TTTGAATTTGTTTGTTGATTTACCATATCTATTGAATGAGTTTGCTATGTTGGCGTTTCAAGGAC
894665 TACTATTCTTGAGTTTTAACTTTCTAAAGCATCAATGCGATTTTGAATCTCTTCAAAAATGATTT
131 TACTATTCTTGAGTTTTAACTTTCTAAAGCATCAATGCGATTTTGAATCTCTTCAAAAATGATTT
894730 TGAATGATTATGCACAAATGGCCAAGTACAAGCCATAAATGTGATAAATTCCATCCAATCACACA
196 TGAATGATTATGCACAAATGGCCAAGTACAAGCCATAAATGTGATAAATTCCATCCAATCACACA
894795 TTGTCCAGGCATGTGAACAGTAAAAGCCAGGGCTAAAATTTGAGTAAAATAAAGTTAAAAAATTA
261 TTGTCCAGGCATGTGAACAGTAAAAGCCA-GGCTAAAATTTGAGTAAAATAAAGTTAAAAAATTA
*
894860 TCAGGAAAAATGATGATGGTTCAGCTAAGATCAGCCCACAGAGCCATTTTGGATCCAAGCGGCAC
325 TCAAGAAAAATGATGATGGTTCAGCTAAGATCAGCCCACAGAGCCATTTTGGATCCAAGCGGCAC
*
894925 CGGCCTGTTATCCTTCCACTGC-AAGAGCGGGAAGTCTTCTCTGTGAATCCAGCCTCAC
390 CAGCCTGTTATCCTTCCACTGCAAAGAGCGGGAAGTCTTCTCTGTGAATCCAGCCTCAC
894983 ACGCGGTCCT
Statistics
Matches: 441, Mismatches: 6, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
462 17 0.04
464 1 0.00
465 2 0.00
467 303 0.69
468 118 0.27
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (462 bp):
TTGAGTAAAAGAGTTTTTTAGATTCTTTTCAAACCATTTTGCTAATTTGTTGATTATCAGAATCA
TTTGAATTTGTTTGTTGATTTACCATATCTATTGAATGAGTTTGCTATGTTGGCGTTTCAAGGAC
TACTATTCTTGAGTTTTAACTTTCTAAAGCATCAATGCGATTTTGAATCTCTTCAAAAATGATTT
TGAATGATTATGCACAAATGGCCAAGTACAAGCCATAAATGTGATAAATTCCATCCAATCACACA
TTGTCCAGGCATGTGAACAGTAAAAGCCAGGCTAAAATTTGAGTAAAATAAAGTTAAAAAATTAT
CAAGAAAAATGATGATGGTTCAGCTAAGATCAGCCCACAGAGCCATTTTGGATCCAAGCGGCACC
AGCCTGTTATCCTTCCACTGCAAAGAGCGGGAAGTCTTCTCTGTGAATCCAGCCTCACGCGGTGC
CCTCCAC
Found at i:896526 original size:7 final size:7
Alignment explanation
Indices: 896514--896564 Score: 93
Period size: 7 Copynumber: 7.3 Consensus size: 7
896504 GCATCTTCAG
*
896514 AACTATA
1 AACTATC
896521 AACTATC
1 AACTATC
896528 AACTATC
1 AACTATC
896535 AACTATC
1 AACTATC
896542 AACTATC
1 AACTATC
896549 AACTATC
1 AACTATC
896556 AACTATC
1 AACTATC
896563 AA
1 AA
896565 AGACATAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (7 bp):
AACTATC
Found at i:900097 original size:2 final size:2
Alignment explanation
Indices: 900092--900132 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
900082 TTTAACGAGC
900092 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
900133 CTCACAGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:904434 original size:33 final size:33
Alignment explanation
Indices: 904384--904469 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
904374 AAATAAATTA
* *
904384 AAATAAAATATATAATATA-AAAATTATAGTAAAC
1 AAATAAAA-ATAAAATATATAAAATTATAAT-AAC
* *
904418 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATATAAAATTATAATAAC
*
904451 AAATGAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
904470 GNNNNNNNNN
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 29 0.63
34 17 0.37
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAC
Found at i:912369 original size:2 final size:2
Alignment explanation
Indices: 912364--912404 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
912354 CATCTCTCCT
* *
912364 TA TA TA TT TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
912405 GTTGTGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:922767 original size:3 final size:3
Alignment explanation
Indices: 922754--922786 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
922744 AAGTAGTGTC
*
922754 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
922787 TAAAAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:936174 original size:21 final size:22
Alignment explanation
Indices: 936150--936201 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
936140 AAATTTATTT
936150 AATTAAAAATAAAAAT-ATAAA
1 AATTAAAAATAAAAATAATAAA
*
936171 AATT-AAAATAAATATAATAAA
1 AATTAAAAATAAAAATAATAAA
936192 AATTAAAAAT
1 AATTAAAAAT
936202 TTTCTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AATTAAAAATAAAAATAATAAA
Found at i:940862 original size:32 final size:35
Alignment explanation
Indices: 940825--940896 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 35
940815 TGTAATGTCG
* *
940825 TTTAAGTTGTTTTTTG-GAT-TTT-TTTTCTG-TTA
1 TTTAAGTTGATATTTGAGATATTTGTTTT-TGATTA
940857 TTTAAGTTGATATTTGAGATATTTGTTTTTGATTA
1 TTTAAGTTGATATTTGAGATATTTGTTTTTGATTA
940892 TTTAA
1 TTTAA
940897 AATTAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 14 0.41
33 3 0.09
34 5 0.15
35 12 0.35
ACGTcount: A:0.21, C:0.01, G:0.15, T:0.62
Consensus pattern (35 bp):
TTTAAGTTGATATTTGAGATATTTGTTTTTGATTA
Found at i:941253 original size:25 final size:27
Alignment explanation
Indices: 941198--941256 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
941188 ACTGCTGATG
*
941198 TGGCAATTACTTAATTAAAAAAATGACT
1 TGGCAATTACTTAATT-AAAAAATGAAT
*
941226 TGGCAATTGCTTAATT-AAAAA-GAAT
1 TGGCAATTACTTAATTAAAAAATGAAT
941251 TGGCAA
1 TGGCAA
941257 AAAAGTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.31
26 5 0.17
28 15 0.52
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (27 bp):
TGGCAATTACTTAATTAAAAAATGAAT
Found at i:946420 original size:3 final size:3
Alignment explanation
Indices: 946412--946445 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
946402 AACCACAGCT
946412 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
946446 CACAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:947416 original size:210 final size:211
Alignment explanation
Indices: 947054--947465 Score: 596
Period size: 210 Copynumber: 2.0 Consensus size: 211
947044 TAAAAATTAT
* * * * * *
947054 CATACTATATAAAATTATTATGAATATTTTTGTGAATGTCTATTTATATTATCTATATTTAAATT
1 CATACTACATAAAATTATTATGAATATTTTTATAAATATCCATTTATATTATCTATATTTAAATG
*
947119 TGGATGTAAATTAGATTGGATCAACATTAGGATTTAATCCATCTAATCGTTAAGTATTATCTTCA
66 TAGATGTAAATTAGATTGGATCAACATTAGGATTTAATCCATCTAATCGTTAAGTATTATCTTCA
* ** **
947184 TCTTATAAATTCTATCTAAATAAGGGGTTATAT-ACTATAAATAGGTCTTTCACTTCATTTGTAA
131 TCTTATAAATTCTATCTAAATAAAGGGTTATATGACTATAAATAGACCCCTCACTTCATTTGTAA
*
947248 GGACACACTTCAATAA
196 AGACACACTTCAATAA
* * *
947264 CATACTACATAAATTTATTATGAATATTTTTATAAATATCCATTTATGTTATCTATATTTAGATG
1 CATACTACATAAAATTATTATGAATATTTTTATAAATATCCATTTATATTATCTATATTTAAATG
* * * *
947329 TAGATGTAAATTAGATTGGATCAACATTAGGATTTAATCTATCTGATCTTTGAGTATTAT-TATC
66 TAGATGTAAATTAGATTGGATCAACATTAGGATTTAATCCATCTAATCGTTAAGTATTATCT-TC
*
947393 AT-TTAATAAATTCTATCTAAATAAAGGGTTATATGCCTATAAATAGACCCCTCACTTCATTTGT
130 ATCTT-ATAAATTCTATCTAAATAAAGGGTTATATGACTATAAATAGACCCCTCACTTCATTTGT
947457 AAAGACACA
194 AAAGACACA
947466 TATCATTAAC
Statistics
Matches: 178, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
209 3 0.02
210 143 0.80
211 32 0.18
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (211 bp):
CATACTACATAAAATTATTATGAATATTTTTATAAATATCCATTTATATTATCTATATTTAAATG
TAGATGTAAATTAGATTGGATCAACATTAGGATTTAATCCATCTAATCGTTAAGTATTATCTTCA
TCTTATAAATTCTATCTAAATAAAGGGTTATATGACTATAAATAGACCCCTCACTTCATTTGTAA
AGACACACTTCAATAA
Found at i:947937 original size:26 final size:26
Alignment explanation
Indices: 947907--948004 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 26
947897 AAAAAAAAAA
947907 TACCACTAGAAGTGGATGGATAATTT
1 TACCACTAGAAGTGGATGGATAATTT
** ***
947933 TACCAGC-AGAA-TCTAAAAATAATTT
1 TACCA-CTAGAAGTGGATGGATAATTT
* * *
947958 TACTATTAGAAGTAGATGGATAATTT
1 TACCACTAGAAGTGGATGGATAATTT
947984 TACCA-TCAGAAGTGGATGGAT
1 TACCACT-AGAAGTGGATGGAT
948005 CTCTTAACTC
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
25 18 0.33
26 35 0.65
27 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (26 bp):
TACCACTAGAAGTGGATGGATAATTT
Found at i:948064 original size:17 final size:17
Alignment explanation
Indices: 948042--948084 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
948032 CACGTGGATC
948042 ACCTACCAATACTTGTA
1 ACCTACCAATACTTGTA
948059 ACCTACCAATACTTGTA
1 ACCTACCAATACTTGTA
*
948076 ACCCACCAA
1 ACCTACCAA
948085 AAGTAGATGA
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:0.37, C:0.35, G:0.05, T:0.23
Consensus pattern (17 bp):
ACCTACCAATACTTGTA
Found at i:948110 original size:28 final size:28
Alignment explanation
Indices: 948066--948125 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
948056 GTAACCTACC
*
948066 AATACTTGTAACCCACCAAAAGTAGATG
1 AATACTTGTAACCCACCAAAAGTAGATA
* * * *
948094 AATACTTTTAACTCACCAGAAGTTGATA
1 AATACTTGTAACCCACCAAAAGTAGATA
948122 AATA
1 AATA
948126 ATAAAAAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (28 bp):
AATACTTGTAACCCACCAAAAGTAGATA
Found at i:948144 original size:14 final size:14
Alignment explanation
Indices: 948118--948155 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
948108 ACCAGAAGTT
948118 GATAAATAATAAAAA
1 GATAAA-AATAAAAA
948133 GATAAAAATAAAAA
1 GATAAAAATAAAAA
948147 GTATAAAAA
1 G-ATAAAAA
948156 GAATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (14 bp):
GATAAAAATAAAAA
Found at i:948248 original size:21 final size:21
Alignment explanation
Indices: 948224--948265 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
948214 TATCCATTTT
948224 GTATTTTATCAAGTATCATTG
1 GTATTTTATCAAGTATCATTG
948245 GTATTTTATCAAGTATCATTG
1 GTATTTTATCAAGTATCATTG
948266 AAAACTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (21 bp):
GTATTTTATCAAGTATCATTG
Found at i:952450 original size:23 final size:24
Alignment explanation
Indices: 952418--952462 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
952408 CTTTCTGTAA
*
952418 TTATTTTTTTAAATTAT-TTTTAT
1 TTATTCTTTTAAATTATATTTTAT
*
952441 TTATTCTTTTAAGTTATATTTT
1 TTATTCTTTTAAATTATATTTT
952463 CATAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTATTCTTTTAAATTATATTTTAT
Found at i:957254 original size:22 final size:22
Alignment explanation
Indices: 957226--957268 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
957216 TAGAAACCCG
957226 TGCAAGAATATTCATTAATTGT
1 TGCAAGAATATTCATTAATTGT
957248 TGCAAGAATATTCATTAATTG
1 TGCAAGAATATTCATTAATTG
957269 ATGTGTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
TGCAAGAATATTCATTAATTGT
Found at i:960277 original size:2 final size:2
Alignment explanation
Indices: 960270--960320 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
960260 TTGATGATTG
960270 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
960312 AT AT AT AT A
1 AT AT AT AT A
960321 GCCATGTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:960777 original size:2 final size:2
Alignment explanation
Indices: 960756--960797 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
960746 GAACCATGAA
* * *
960756 AT AT CT AT AT AC AT AC 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
960798 GTTTGCCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:967723 original size:2 final size:2
Alignment explanation
Indices: 967716--967742 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
967706 AGGAAAACAG
967716 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
967743 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:975078 original size:27 final size:25
Alignment explanation
Indices: 975040--975090 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
975030 CACATAATTT
975040 ATTTTTTAGTAAAAAATATTAAACACC
1 ATTTTTTAGT-AAAAATA-TAAACACC
975067 ATTTTTTAGTAAAAATATAAACAC
1 ATTTTTTAGTAAAAATATAAACAC
975091 TATATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 10 0.42
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTTTTTAGTAAAAATATAAACACC
Found at i:987696 original size:16 final size:17
Alignment explanation
Indices: 987657--987691 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
987647 TGAGGGAAAA
987657 AAAATTAAAAA-AAATT
1 AAAATTAAAAATAAATT
987673 AAAATTAAAAATAAATT
1 AAAATTAAAAATAAATT
987690 AA
1 AA
987692 TTTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTAAAAATAAATT
Done.