Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 92 of 106
Found at i:19231670 original size:24 final size:27
Alignment explanation
Indices: 19231598--19231671 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
19231588 ATATCATATT
*
19231598 TAATA-ATTTAAAATAAATAATT-ATAAA
1 TAATATATTTAATATAAAT--TTAATAAA
* *
19231625 TAATATATTTGATATAATTTTAATAAA
1 TAATATATTTAATATAAATTTAATAAA
19231652 TAAT-TA-TTAATA-AAATTTAA
1 TAATATATTTAATATAAATTTAA
19231672 ATTTAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.17
25 5 0.12
26 4 0.10
27 14 0.35
28 10 0.25
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TAATATATTTAATATAAATTTAATAAA
Found at i:19232817 original size:17 final size:19
Alignment explanation
Indices: 19232775--19232817 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
19232765 TTAAATCGAA
*
19232775 TTATATATTTGTATTAATT
1 TTATATATTTGTATTAAAT
19232794 TTATATATTT-T-TTAAAT
1 TTATATATTTGTATTAAAT
*
19232811 TTGTATA
1 TTATATA
19232818 AAATGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATATATTTGTATTAAAT
Found at i:19234148 original size:3 final size:3
Alignment explanation
Indices: 19234140--19234174 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19234130 TTGATCATGA
19234140 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
19234175 TTCTTCTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:19243420 original size:21 final size:20
Alignment explanation
Indices: 19243392--19243431 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19243382 TTCTAATAAT
*
19243392 ATTATACTTTTATTATATCG
1 ATTATACTTTAATTATATCG
*
19243412 ATTAGTACTTTAATTCTATC
1 ATTA-TACTTTAATTATATC
19243432 TATGCTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTATACTTTAATTATATCG
Found at i:19248115 original size:24 final size:24
Alignment explanation
Indices: 19248085--19248130 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19248075 GATAAGAGTT
19248085 TATATTTGATATATTATCAATATA
1 TATATTTGATATATTATCAATATA
* *
19248109 TATATTTTATATATTATTAATA
1 TATATTTGATATATTATCAATA
19248131 AATCAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TATATTTGATATATTATCAATATA
Found at i:19254284 original size:3 final size:3
Alignment explanation
Indices: 19254276--19254328 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
19254266 GCACAGGGCG
* * *
19254276 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCG GCA GCC GCA GCC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
19254324 GCA GC
1 GCA GC
19254329 TGCTGTTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.26, C:0.38, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:19255062 original size:16 final size:16
Alignment explanation
Indices: 19255043--19255094 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
19255033 AAATTAGTTC
19255043 ATTTAATAATTTTAAA
1 ATTTAATAATTTTAAA
*
19255059 ATTTAAT-ATTTAATAA
1 ATTTAATAATTTTA-AA
19255075 ATTT-A-AATTTTAAA
1 ATTTAATAATTTTAAA
*
19255089 AATTAA
1 ATTTAA
19255095 ATACTTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.17
15 12 0.40
16 13 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAATAATTTTAAA
Found at i:19255069 original size:23 final size:23
Alignment explanation
Indices: 19255043--19255087 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19255033 AAATTAGTTC
*
19255043 ATTTAATAATTTTAAAATTTAAT
1 ATTTAATAAATTTAAAATTTAAT
*
19255066 ATTTAATAAATTTAAATTTTAA
1 ATTTAATAAATTTAAAATTTAA
19255088 AAATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAATAAATTTAAAATTTAAT
Found at i:19255094 original size:23 final size:23
Alignment explanation
Indices: 19255045--19255094 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
19255035 ATTAGTTCAT
* * *
19255045 TTAATAATTTTAAAATTTAATAT
1 TTAATAAATTTAAAATTTAAAAA
*
19255068 TTAATAAATTTAAATTTTAAAAA
1 TTAATAAATTTAAAATTTAAAAA
19255091 TTAA
1 TTAA
19255095 ATACTTACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATAAATTTAAAATTTAAAAA
Found at i:19255599 original size:13 final size:13
Alignment explanation
Indices: 19255569--19255602 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19255559 AATAATTAAA
19255569 TAAAAATTAAAAC
1 TAAAAATTAAAAC
* *
19255582 AAAAAATTAAAAT
1 TAAAAATTAAAAC
19255595 TAAAAATT
1 TAAAAATT
19255603 TTCTTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAATTAAAAC
Found at i:19255768 original size:13 final size:12
Alignment explanation
Indices: 19255735--19255759 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19255725 TTGAATTATA
19255735 AATAATATTTTT
1 AATAATATTTTT
19255747 AATAATATTTTT
1 AATAATATTTTT
19255759 A
1 A
19255760 TATATTATTG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATAATATTTTT
Found at i:19271467 original size:17 final size:17
Alignment explanation
Indices: 19271441--19271482 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
19271431 TATTAACATA
* *
19271441 AAATTTTTAATATTAAT
1 AAATTTTAAATAATAAT
19271458 AATATTTTAAATAATAAT
1 AA-ATTTTAAATAATAAT
19271476 AAATTTT
1 AAATTTT
19271483 GAGTGTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTTAAATAATAAT
Found at i:19273044 original size:20 final size:20
Alignment explanation
Indices: 19273019--19273064 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
19273009 ATAAATAAAT
19273019 CTTAAACAAATATAAACGAA
1 CTTAAACAAATATAAACGAA
* *
19273039 CTTAAATAAATATAAATGAA
1 CTTAAACAAATATAAACGAA
*
19273059 TTTAAA
1 CTTAAA
19273065 ATAAGATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (20 bp):
CTTAAACAAATATAAACGAA
Found at i:19273519 original size:63 final size:63
Alignment explanation
Indices: 19273446--19273571 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
19273436 TGAAACATGG
*
19273446 TTCAAGTATAATAAATGTATAAATACATACATTAATACTGTATTATCATTGAAAATAATTGAA
1 TTCAAGTATAATAAATGTATAAATACATACAATAATACTGTATTATCATTGAAAATAATTGAA
** * *
19273509 TTCAAGTATAATAAATGTATAAATGTATGCAATAATACTGTATTATGATTGAAAATAATTGAA
1 TTCAAGTATAATAAATGTATAAATACATACAATAATACTGTATTATCATTGAAAATAATTGAA
19273572 GAAGTAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (63 bp):
TTCAAGTATAATAAATGTATAAATACATACAATAATACTGTATTATCATTGAAAATAATTGAA
Found at i:19274617 original size:2 final size:2
Alignment explanation
Indices: 19274568--19274598 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19274558 TATGTGTTTG
19274568 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 T
19274599 GAGAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19276026 original size:16 final size:16
Alignment explanation
Indices: 19276005--19276037 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19275995 ACATCTATTG
*
19276005 AAATTAATAATTAAAA
1 AAATTAAAAATTAAAA
19276021 AAATTAAAAATTAAAA
1 AAATTAAAAATTAAAA
19276037 A
1 A
19276038 TTTTATACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTAAAAATTAAAA
Found at i:19281847 original size:15 final size:15
Alignment explanation
Indices: 19281823--19281852 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19281813 TGTTTAATTA
*
19281823 TAATTGAATTTAAAT
1 TAATTAAATTTAAAT
19281838 TAATTAAATTTAAAT
1 TAATTAAATTTAAAT
19281853 ATTGTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TAATTAAATTTAAAT
Found at i:19289290 original size:33 final size:33
Alignment explanation
Indices: 19289253--19289319 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
19289243 ATCAATACAA
*
19289253 AGAAATAAACTTAAAACTACTCCATCATATTCT
1 AGAAATAAACTTAAAACTAATCCATCATATTCT
19289286 AGAAATAAACTTAAAACTAATCCATCATATTCT
1 AGAAATAAACTTAAAACTAATCCATCATATTCT
19289319 A
1 A
19289320 ACTTGTAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (33 bp):
AGAAATAAACTTAAAACTAATCCATCATATTCT
Found at i:19291886 original size:16 final size:16
Alignment explanation
Indices: 19291865--19291899 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19291855 TCCGCAATCC
*
19291865 TCTCCTCCCCTAAGCA
1 TCTCCTCCACTAAGCA
19291881 TCTCCTCCACTAAGCA
1 TCTCCTCCACTAAGCA
19291897 TCT
1 TCT
19291900 AACCTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.46, G:0.06, T:0.29
Consensus pattern (16 bp):
TCTCCTCCACTAAGCA
Found at i:19297468 original size:15 final size:15
Alignment explanation
Indices: 19297444--19297474 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19297434 TGTTTAATTA
*
19297444 TAATTGAATTTAAAT
1 TAATTAAATTTAAAT
19297459 TAATTAAATTTAAAT
1 TAATTAAATTTAAAT
19297474 T
1 T
19297475 TGTTATAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TAATTAAATTTAAAT
Found at i:19301561 original size:1 final size:1
Alignment explanation
Indices: 19301557--19301593 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
19301547 CTTTCTTTTT
19301557 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19301594 GGAGAAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19304963 original size:33 final size:33
Alignment explanation
Indices: 19304926--19304992 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
19304916 ATCAATACAA
* *
19304926 AGAAATAAACTTAAAACTACTCCATCATATTCT
1 AGAAATAAACTTAAAACTAATCCAACATATTCT
19304959 AGAAATAAACTTAAAACTAATCCAACATATTCT
1 AGAAATAAACTTAAAACTAATCCAACATATTCT
19304992 A
1 A
19304993 ACTTGTAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.28
Consensus pattern (33 bp):
AGAAATAAACTTAAAACTAATCCAACATATTCT
Found at i:19307570 original size:16 final size:16
Alignment explanation
Indices: 19307549--19307583 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19307539 TCCGCAATCC
*
19307549 TCTCCTCCCCTAAGCA
1 TCTCCTCCACTAAGCA
19307565 TCTCCTCCACTAAGCA
1 TCTCCTCCACTAAGCA
19307581 TCT
1 TCT
19307584 AACCTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.46, G:0.06, T:0.29
Consensus pattern (16 bp):
TCTCCTCCACTAAGCA
Found at i:19310902 original size:29 final size:29
Alignment explanation
Indices: 19310870--19310928 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
19310860 AAGAAACAAT
*
19310870 TAAATTTAATTGGTTTATATTATTGAAAA
1 TAAATTTAATTGGTTTATAATATTGAAAA
19310899 TAAATTTAATTGGTTTATAATATTGAAAA
1 TAAATTTAATTGGTTTATAATATTGAAAA
19310928 T
1 T
19310929 TTATCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (29 bp):
TAAATTTAATTGGTTTATAATATTGAAAA
Found at i:19312202 original size:17 final size:17
Alignment explanation
Indices: 19312156--19312241 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
19312146 ATTTGTCAAG
*
19312156 TTATTTTTTATCAATTTT
1 TTATTTTTT-TTAATTTT
** *
19312174 TTATTTACTTTATTTTT
1 TTATTTTTTTTAATTTT
*
19312191 TTATTTTTTTTAAAATTT
1 TTATTTTTTTT-AATTTT
* *
19312209 ATATATTCTTTTAATATTT
1 TTAT-TTTTTTTAAT-TTT
*
19312228 TTAATTTTTTTAAT
1 TTATTTTTTTTAAT
19312242 GCGAGATCCA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
17 15 0.29
18 25 0.49
19 11 0.22
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTTTTAATTTT
Found at i:19312222 original size:19 final size:18
Alignment explanation
Indices: 19312198--19312240 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
19312188 TTTTTATTTT
19312198 TTTTAAAATTTATATATTC
1 TTTTAAAATTTATA-ATTC
* * *
19312217 TTTTAATATTTTTAATTT
1 TTTTAAAATTTATAATTC
19312235 TTTTAA
1 TTTTAA
19312241 TGCGAGATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAAAATTTATAATTC
Found at i:19312525 original size:28 final size:28
Alignment explanation
Indices: 19312469--19312532 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
19312459 AATTTATAAC
**
19312469 AAAAA-ATTAATAAATAAAAAAATTTTA
1 AAAAATATTAATAAATAAAAAAATAATA
*
19312496 AAAAATATTAATAAA-AATATAAATAATA
1 AAAAATATTAATAAATAA-AAAAATAATA
19312524 AAATAATAT
1 AAA-AATAT
19312533 GTATTCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 7 0.23
28 19 0.61
29 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAATATTAATAAATAAAAAAATAATA
Found at i:19312614 original size:20 final size:21
Alignment explanation
Indices: 19312575--19312616 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
19312565 ATAAATAAAT
* *
19312575 ATTTTATTTAAAATATAATCA
1 ATTTTATTTAAAACAAAATCA
19312596 ATTTT-TTTAAAACAAAATCA
1 ATTTTATTTAAAACAAAATCA
19312616 A
1 A
19312617 GTCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTATTTAAAACAAAATCA
Found at i:19315880 original size:33 final size:33
Alignment explanation
Indices: 19315843--19315909 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
19315833 ATCAATACAA
*
19315843 AGAAATAAACTTAAAACTACTCCATCATATTCT
1 AGAAATAAACTTAAAACTAATCCATCATATTCT
19315876 AGAAATAAACTTAAAACTAATCCATCATATTCT
1 AGAAATAAACTTAAAACTAATCCATCATATTCT
19315909 A
1 A
19315910 ACTTGTAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (33 bp):
AGAAATAAACTTAAAACTAATCCATCATATTCT
Found at i:19318484 original size:16 final size:16
Alignment explanation
Indices: 19318459--19318490 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19318449 GCAATCCTCC
*
19318459 CCTCCCCTAAGCATCT
1 CCTCCACTAAGCATCT
19318475 CCTCCACTAAGCATCT
1 CCTCCACTAAGCATCT
19318491 AACCTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25
Consensus pattern (16 bp):
CCTCCACTAAGCATCT
Found at i:19319728 original size:11 final size:11
Alignment explanation
Indices: 19319712--19319751 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
19319702 AATCTCATAA
19319712 GAGATTTGTTT
1 GAGATTTGTTT
*
19319723 GAGATTTGTTA
1 GAGATTTGTTT
19319734 GAGATTTGTTT
1 GAGATTTGTTT
*
19319745 AAGATTT
1 GAGATTT
19319752 TTCAGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:19319934 original size:52 final size:52
Alignment explanation
Indices: 19319790--19319934 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 52
19319780 CTTGCAAAAA
* * *
19319790 AAGAATTCTAAGA-GAAAGAGGATTCTTAATAGGTAAGTTTAACTTGCAAGAG
1 AAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTTGACTTACAAGAG
* * *
19319842 AAGAATTCTAAAAGGAAATGGATTCTTAATAGGCAAGTTTGACTTACAGGAG
1 AAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTGACTTACAAGAG
* *
19319894 AAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTTG
1 AAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTG
19319935 TATGGTTATA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 78 0.95
53 4 0.05
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (52 bp):
AAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTTGACTTACAAGAG
Found at i:19322786 original size:12 final size:12
Alignment explanation
Indices: 19322753--19322788 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19322743 TCCGGATCAA
**
19322753 ATTATTATTACT
1 ATTATTATTGTT
19322765 ATTATTATTGTT
1 ATTATTATTGTT
19322777 ATTATTATTGTT
1 ATTATTATTGTT
19322789 TAATGAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:19323393 original size:2 final size:2
Alignment explanation
Indices: 19323340--19323378 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19323330 TACAAATCCA
19323340 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
19323379 AAGAGAAAAT
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:19336744 original size:14 final size:16
Alignment explanation
Indices: 19336727--19336759 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19336717 TTAGTTTGAA
19336727 AATAT-AAA-AATTAT
1 AATATAAAATAATTAT
19336741 AATATAAAATAATTAT
1 AATATAAAATAATTAT
19336757 AAT
1 AAT
19336760 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 3 0.18
16 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:19338338 original size:14 final size:14
Alignment explanation
Indices: 19338321--19338348 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19338311 CTACAAATCC
19338321 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
19338335 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
19338349 GAGAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:19344604 original size:30 final size:29
Alignment explanation
Indices: 19344570--19344634 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
19344560 CGACTCCTCT
* *
19344570 TCTTCACAACCAACCACCTCTCTCTTTGG-C
1 TCTTCACAACC-ACCACATCGCT-TTTGGCC
*
19344600 TCTTCCACATCCACCACATCGCTTTTGGCC
1 TCTT-CACAACCACCACATCGCTTTTGGCC
19344630 TCTTC
1 TCTTC
19344635 TTCACTCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 6 0.20
30 18 0.60
31 6 0.20
ACGTcount: A:0.17, C:0.43, G:0.08, T:0.32
Consensus pattern (29 bp):
TCTTCACAACCACCACATCGCTTTTGGCC
Found at i:19345744 original size:29 final size:27
Alignment explanation
Indices: 19345683--19345745 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
19345673 CTTAATATTA
*
19345683 GATTTTATCATAATACTTCAATTTTAT
1 GATTTTATCATAATACTTCAATTTCAT
*
19345710 GAATTTTATCATTATACTTTCAATTTCATT
1 G-ATTTTATCATAATAC-TTCAATTTCA-T
19345740 GATTTT
1 GATTTT
19345746 TGGATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 14 0.45
29 14 0.45
30 2 0.06
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (27 bp):
GATTTTATCATAATACTTCAATTTCAT
Found at i:19346376 original size:21 final size:21
Alignment explanation
Indices: 19346351--19346412 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
19346341 ATAAATTTTA
19346351 ATTTAATTAA-TTTATATAATT
1 ATTTAATTAATTTTA-ATAATT
*
19346372 ATTTAATAAATTTTAATAATT
1 ATTTAATTAATTTTAATAATT
*
19346393 TTTTAATTTAAATTTTAATA
1 ATTTAA-TT-AATTTTAATA
19346413 CCTATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 20 0.57
22 5 0.14
23 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTAATTTTAATAATT
Found at i:19349284 original size:66 final size:66
Alignment explanation
Indices: 19349200--19349331 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
19349190 ACATTGGAGG
* *
19349200 ACTAAAGGCCTAACTTTAATCAGCAATCAATTAAACGATCTTGAATCTGAAATATCAGATAAACT
1 ACTAAAGGCCTAACTTTAATCAGCAATCAATAAAACGATCTGGAATCTGAAATATCAGATAAACT
19349265 A
66 A
* * * * *
19349266 ACTAAAGGTCTAAGTTTAATCTGCAATCAATAAAACGATCTGGATTCTGAAATTTCAGATAAACT
1 ACTAAAGGCCTAACTTTAATCAGCAATCAATAAAACGATCTGGAATCTGAAATATCAGATAAACT
19349331 A
66 A
19349332 TCATTTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (66 bp):
ACTAAAGGCCTAACTTTAATCAGCAATCAATAAAACGATCTGGAATCTGAAATATCAGATAAACT
A
Found at i:19362617 original size:25 final size:26
Alignment explanation
Indices: 19362588--19362647 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
19362578 AACTATTATT
*
19362588 TGAT-ATTGCTAACA-TAATGATCTCA
1 TGATAATTGCT-ACATTAATGATCTAA
*
19362613 TGATAATTG-TGCATTAATGATCTAA
1 TGATAATTGCTACATTAATGATCTAA
19362638 TGATAATTGC
1 TGATAATTGC
19362648 GCATTCTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 24 0.80
26 4 0.13
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (26 bp):
TGATAATTGCTACATTAATGATCTAA
Found at i:19362651 original size:25 final size:25
Alignment explanation
Indices: 19362602--19362652 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19362592 ATTGCTAACA
* *
19362602 TAATGATCTCATGATAATTGTGCAT
1 TAATGATCTAATGATAATTGCGCAT
19362627 TAATGATCTAATGATAATTGCGCAT
1 TAATGATCTAATGATAATTGCGCAT
19362652 T
1 T
19362653 CTTGGTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (25 bp):
TAATGATCTAATGATAATTGCGCAT
Found at i:19363281 original size:47 final size:47
Alignment explanation
Indices: 19363197--19363290 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
19363187 ATATTTACTT
* * *
19363197 AAGGGTTATTTTGGGAAAGTGAATACCTCCTTATCTTTCTCTCTCTC
1 AAGGGTTATTCTGGGAAAGTGAATACCCCCATATCTTTCTCTCTCTC
*
19363244 AAGGGTTATTCTGGG-AAGTGAATCCCCCCATATTCTTTCTCTCTCTC
1 AAGGGTTATTCTGGGAAAGTGAATACCCCCATA-TCTTTCTCTCTCTC
19363291 TCTCTCTCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 14 0.33
47 28 0.67
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (47 bp):
AAGGGTTATTCTGGGAAAGTGAATACCCCCATATCTTTCTCTCTCTC
Found at i:19370408 original size:28 final size:30
Alignment explanation
Indices: 19370349--19370418 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
19370339 GAATATTTCA
*
19370349 TAAATTATTATAAAATATTTAATGTAAAATT
1 TAAATTA-TAAAAAATATTTAATGTAAAATT
* *
19370380 TAAATT-TAAAAAAT-TTTAATGTGATATT
1 TAAATTATAAAAAATATTTAATGTAAAATT
*
19370408 TTAATTATAAA
1 TAAATTATAAA
19370419 TATGATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 17 0.50
29 11 0.32
31 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (30 bp):
TAAATTATAAAAAATATTTAATGTAAAATT
Found at i:19376473 original size:94 final size:93
Alignment explanation
Indices: 19376301--19376484 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 93
19376291 GATGCCTTTA
*
19376301 TGCAAATATTGAAGTTGTTGGTTGTGGGGGACAGTGTGCAAACCCACGTGACAATTTGCATTAAA
1 TGCAAATATTGAAGTTGTCGGTTGTGGGGGACAGTGTGCAAACCCACGTGACAATTTGCATTAAA
*
19376366 ATAATTAATGTTATAAATTATTTTTGGG
66 ATAATTAATGTTATAAATGATTTTTGGG
* * *
19376394 TGCAAATATTATAAGTTGTCGGTTGTGGGGGACCGTGTGCAAACCCACGTGACAATTTGCTTTAA
1 TGCAAATATT-GAAGTTGTCGGTTGTGGGGGACAGTGTGCAAACCCACGTGACAATTTGCATTAA
19376459 AATAATTAATGTTATAAATGATTTTT
65 AATAATTAATGTTATAAATGATTTTT
19376485 AAATTATAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
93 10 0.12
94 75 0.88
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (93 bp):
TGCAAATATTGAAGTTGTCGGTTGTGGGGGACAGTGTGCAAACCCACGTGACAATTTGCATTAAA
ATAATTAATGTTATAAATGATTTTTGGG
Found at i:19376581 original size:31 final size:32
Alignment explanation
Indices: 19376519--19376583 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
19376509 TTAAAAATTT
* *
19376519 TTAATATGATATTTGAATTATAAAATTATTAA
1 TTAATATGACATTTGAATTATAAAATGATTAA
* *
19376551 TTAATATGACATTT-ATTTATAATATGATTAA
1 TTAATATGACATTTGAATTATAAAATGATTAA
19376582 TT
1 TT
19376584 TTAAATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (32 bp):
TTAATATGACATTTGAATTATAAAATGATTAA
Found at i:19376689 original size:27 final size:28
Alignment explanation
Indices: 19376617--19376696 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
19376607 TAAATAATTT
* *
19376617 TTTAAATATTATATTAATAATAATTTATAA
1 TTTAAATATTATATTAA-AA-ATTTTAAAA
*
19376647 TTTAAATATCATATTAAAAATTTTAAAA
1 TTTAAATATTATATTAAAAATTTTAAAA
19376675 TTTAAATATTA-ATTAAAAATTT
1 TTTAAATATTATATTAAAAATTT
19376697 ATTAATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
27 11 0.24
28 17 0.37
29 2 0.04
30 16 0.35
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAAATATTATATTAAAAATTTTAAAA
Found at i:19377739 original size:20 final size:22
Alignment explanation
Indices: 19377704--19377743 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
19377694 TCTCATTTAA
19377704 CTTTTTATTATTTTTTAATTCT
1 CTTTTTATTATTTTTTAATTCT
19377726 CTTTTT-TT-TTTTTTAATT
1 CTTTTTATTATTTTTTAATT
19377744 TGTAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (22 bp):
CTTTTTATTATTTTTTAATTCT
Found at i:19383124 original size:31 final size:31
Alignment explanation
Indices: 19383089--19383150 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
19383079 AACTGCTGCT
*
19383089 TGAGGTTTTGTTTATCAGTATGTAAAAAAGA
1 TGAGGTTTTGTTTATCAGCATGTAAAAAAGA
19383120 TGAGGTTTTGTTTATCAGCATGTAAAAAAGA
1 TGAGGTTTTGTTTATCAGCATGTAAAAAAGA
19383151 AAAACTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (31 bp):
TGAGGTTTTGTTTATCAGCATGTAAAAAAGA
Found at i:19394321 original size:15 final size:16
Alignment explanation
Indices: 19394292--19394324 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
19394282 AATTAATTAA
19394292 AATTTTATATAAAATT
1 AATTTTATATAAAATT
19394308 AATTTTAT-TAAAATT
1 AATTTTATATAAAATT
19394323 AA
1 AA
19394325 CATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTTATATAAAATT
Found at i:19395405 original size:13 final size:14
Alignment explanation
Indices: 19395382--19395414 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19395372 ATACTAAAAA
19395382 TAAAA-TAAATA-T
1 TAAAATTAAATATT
19395394 TAAAATTAAATATT
1 TAAAATTAAATATT
19395408 TAAAATT
1 TAAAATT
19395415 TTATTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 6 0.32
14 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATTAAATATT
Found at i:19396119 original size:16 final size:15
Alignment explanation
Indices: 19396073--19396124 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
19396063 TTCATTATTA
*
19396073 ATTAAGTTTATAAAT
1 ATTAAGTTCATAAAT
* * *
19396088 ATAAAATTCATGAAT
1 ATTAAGTTCATAAAT
19396103 ATGTAAGTTCATAAAT
1 AT-TAAGTTCATAAAT
19396119 AATTAA
1 -ATTAA
19396125 ATATCAATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 13 0.46
16 13 0.46
17 2 0.07
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (15 bp):
ATTAAGTTCATAAAT
Found at i:19396665 original size:3 final size:3
Alignment explanation
Indices: 19396659--19396712 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
19396649 ACGACGAGAG
* *
19396659 AGA AGA A-A ACGA AGA AGA AGA AGA AGA AGA AGA AGA AGA GGA CGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
19396704 AGA AGA AGA
1 AGA AGA AGA
19396713 GCCGAGGCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.63, C:0.04, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19402183 original size:128 final size:127
Alignment explanation
Indices: 19401927--19402305 Score: 413
Period size: 128 Copynumber: 2.9 Consensus size: 127
19401917 CTCTTTTTGC
* * * **
19401927 TTTATATTTT-AAAATTTCATTTATTATAGAATTTAAGCTAAAAGAAATTGTCTG-TTTAATCTC
1 TTTATATTTTAAAAATTT-ATTTATTATAGAATTCAA-CTACAAGAGATTGTCTGACCT-ATCTC
* ** * *
19401990 ATTTTAAAACTAACAAAAGGAAGGCAAAGGAACATGGCCCCACGTCTTGGCTTGTAACATTTATA
63 ATTTTAAAAC-AA-ACAA-GAAGGCAAAGGATTATGGCCCCACGTCTTGGCTTTTAACATCTATA
19402055 TGA
125 TGA
*
19402058 TTTATATTTTAAAAATTTATTTATTATAGAATTCCAACTACAAGAGATTGTCTGAACCTATCCCA
1 TTTATATTTTAAAAATTTATTTATTATAGAATT-CAACTACAAGAGATTGTCTG-ACCTATCTCA
* * * **
19402123 GTTTAAAACAAACAA-AAGGCAAAGGATTATGGTCCCACGTCTTGGCTTTTGATGTCTATATGA
64 TTTTAAAACAAACAAGAAGGCAAAGGATTATGGCCCCACGTCTTGGCTTTTAACATCTATATGA
** * *
19402186 TTTATATTTTAAAAATTTATTTGCTATAAAATTTCAACTACAAGAGATTGTTTTGACCTATCTCA
1 TTTATATTTTAAAAATTTATTTATTATAGAA-TTCAACTACAAGAGATTG-TCTGACCTATCTCA
*
19402251 TTTTAAAACAAACAAAAGTAAGGCAAAGGATTATGGCCCCCCATGTCTTGGCTTT
64 TTTTAAAACAAAC--AAG-AAGGCAAAGGATTATGG--CCCCACGTCTTGGCTTT
19402306 CATGTATACT
Statistics
Matches: 212, Mismatches: 24, Indels: 21
0.82 0.09 0.08
Matches are distributed among these distances:
128 105 0.50
129 5 0.02
130 5 0.02
131 42 0.20
132 39 0.18
133 1 0.00
134 15 0.07
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (127 bp):
TTTATATTTTAAAAATTTATTTATTATAGAATTCAACTACAAGAGATTGTCTGACCTATCTCATT
TTAAAACAAACAAGAAGGCAAAGGATTATGGCCCCACGTCTTGGCTTTTAACATCTATATGA
Found at i:19406022 original size:131 final size:130
Alignment explanation
Indices: 19405868--19406251 Score: 515
Period size: 131 Copynumber: 2.9 Consensus size: 130
19405858 AGTACACATG
* * *
19405868 AAAGCCAAGACA-GGGGCTCTAATCTTTTGCTTTCCTTTTGTTTGTTTTAAGATGGGATAGGTTT
1 AAAGCCAAGACATGGGGC-ATAATCCTTTGCCTTCCTTTTGTTTGTTTTAAGATGGGATAGG-TT
*
19405932 AGACAATCTCTTGTAGTTGAAATTCTATAATAAATAAATTTTTAAAATATAAATCATATAGACAT
64 AGACAATCTCTTGTAGTTGAAATTCTATAATAAATAAATTTTTAAAATATAAATCATATAAACAT
19405997 CA
129 CA
* *
19405999 AAAGCCAAGACATGGGGCATAATCCTTTGCCTTCCTTTTGTTTGTTTTAAGGTTGGATAGGCTTA
1 AAAGCCAAGACATGGGGCATAATCCTTTGCCTTCCTTTTGTTTGTTTTAAGATGGGATAGG-TTA
*
19406064 GACAATCTCTTGTAGTT-AGAATTCTATAGTAAATAAATTTTTAAAATATAAATCATATAAACAT
65 GACAATCTCTTGTAGTTGA-AATTCTATAATAAATAAATTTTTAAAATATAAATCATATAAACAT
*
19406128 TA
129 CA
* * * ** * *
19406130 AAAACCAAGGCGTGGGGTCATGTTCCTTTGCCTTCCTTTTGTTAGTTTTAAAATGGGATAGGTTA
1 AAAGCCAAGACATGGGG-CATAATCCTTTGCCTTCCTTTTGTTTGTTTTAAGATGGGATAGGTTA
* * *
19406195 GACAAT-TACTTTTAGTTGAAATTCTATAATAAATGAAA-ATTTAAAATATAAAGCATA
65 GACAATCT-CTTGTAGTTGAAATTCTATAATAAAT-AAATTTTTAAAATATAAATCATA
19406252 AAATTTGTTC
Statistics
Matches: 225, Mismatches: 22, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
130 2 0.01
131 176 0.78
132 47 0.21
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (130 bp):
AAAGCCAAGACATGGGGCATAATCCTTTGCCTTCCTTTTGTTTGTTTTAAGATGGGATAGGTTAG
ACAATCTCTTGTAGTTGAAATTCTATAATAAATAAATTTTTAAAATATAAATCATATAAACATCA
Found at i:19406786 original size:15 final size:15
Alignment explanation
Indices: 19406766--19406821 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
19406756 ATTTATACCT
19406766 TTAAAAAAAGTATAA
1 TTAAAAAAAGTATAA
19406781 TTAAAAAATA-TAATAA
1 TTAAAAAA-AGT-ATAA
*
19406797 TTATTAATAAAAGAATAA
1 TTA--AA-AAAAGTATAA
19406815 TTAAAAA
1 TTAAAAA
19406822 TTAGAATTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
15 11 0.32
16 10 0.29
18 10 0.29
19 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (15 bp):
TTAAAAAAAGTATAA
Found at i:19414171 original size:319 final size:322
Alignment explanation
Indices: 19413522--19414745 Score: 1894
Period size: 320 Copynumber: 3.8 Consensus size: 322
19413512 AGTGTTCTTA
* *
19413522 GCATAGAATGCCTCCGATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
1 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
* *
19413587 AAAAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTGTTAAGATTATTACAGGCATCT
66 --AAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTTTTAAGATTATTAAAGGCATCT
*
19413652 TTTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAAGTATTTTTG
129 TTTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAGGTATTTTTG
* *
19413717 ATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAAGTATTT
194 ATCAAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTATTT
* *
19413782 TTTTATAAAACGCCTTTAATAATTCTCATAATATTTTTGGACTGGATTATTAAAGGCCTTTTTG
259 TTTTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
* *
19413846 GCATAAAATGCCTTCAATAAACAAGCTATTGAAAAAATAAATCGGATTATTGAAGGCGTTTTTTG
1 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
19413911 -AAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTTTTAAGATTATTAAAGGCATCTTT
66 AAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTTTTAAGATTATTAAAGGCATCTTT
* * *
19413975 TAGTAAAAATGCATTCAATAATCTCGTAGTCAAATTTTAAGGGAATTATTGAAGGTATTTTTGAT
131 TAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAGGTATTTTTGAT
19414040 CAAAAAATGCCTTTAC-T-TAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTATTTTT
196 CAAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTATTTTT
19414103 TTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
261 TTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
*
19414165 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGTGTTTTTTG
1 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
*
19414230 AAAAAAAAAAAAAAGCCTTCAATAATTT-CTTTTAAAATTTTTTTACGATTATTAAAGGCATCTT
66 AAAAAAAAAAAAAA-CCTTCAATAATTTCCTTTTAAAATTTTTTTAAGATTATTAAAGGCATCTT
* *
19414294 TTAGTAAAAATGCCTTCAATAATCTCGTAGTCAAATTTT-AAGAGAATTATTGAAGGTATTTTTT
130 TTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAG-GAATTATTGAAGGTATTTTTG
* *
19414358 ATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGATGGTGAGATTATTATAGGTATTT
194 ATCAAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTATTT
*
19414423 TTTTATAAAACGTCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
259 TTTTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
** * ** *
19414487 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATGGATCGGATTATTGAAGGTATTTTCT-
1 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
* * * * ** * *
19414551 AAAAAAAAAAAACACATTCAATAA-TTCATTTTAAAA-ATTTTTAATGATTATTAAAAACGTATT
66 AAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTTTTAA-GATTATTAAAGGCATCTT
* * * * **
19414614 TTAGTAAAACA-ACTTTCAATAATCTCATAATCAAATTTTAAAAGG-ATTATTAAAGGCGTTTTT
130 TTAGTAAAA-ATACCTTCAATAATCTCGTAGTCAAATTTT-AAAGGAATTATTGAAGGTATTTTT
* * **
19414677 GA-CAGAAAAATGCCTTCACTTATAATTTTTATATTAGTGAAGGTGGTGAGATTATTATAGACAT
193 GATCA-AAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTAT
19414741 TTTTT
257 TTTTT
19414746 ACCAAAAACA
Statistics
Matches: 837, Mismatches: 52, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
319 178 0.21
320 263 0.31
321 167 0.20
322 168 0.20
324 61 0.07
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (322 bp):
GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
AAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTTTTAAGATTATTAAAGGCATCTTT
TAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAGGTATTTTTGAT
CAAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTATTTTT
TTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
Found at i:19414573 original size:641 final size:644
Alignment explanation
Indices: 19413522--19414745 Score: 1955
Period size: 641 Copynumber: 1.9 Consensus size: 644
19413512 AGTGTTCTTA
* *
19413522 GCATAGAATGCCTCCGATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
1 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
*
19413587 AAAAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTGTTAAGATTATTACAGGCATCT
66 AAAAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTGTTAAGATTATTAAAGGCATCT
19413652 TTTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAAGTATTTTTG
131 TTTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAAGTATTTTTG
*
19413717 ATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAAGTATTT
196 ATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGATGGTGAGATTATTATAAGTATTT
*
19413782 TTTTATAAAACGCCTTTAATAATTCTCATAATATTTTTGGACTGGATTATTAAAGGCCTTTTTGG
261 TTTTATAAAACGCCTTTAATAATTCTCATAATATTTTTGGACTGGATTATTAAAGGCCCTTTTGG
* * *
19413847 CATAAAATGCCTTCAATAAACAAGCTATTGAAAAAATAAATCGGATTATTGAAGGCGTTTTTTGA
326 CATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAATCGGATTATTGAAGGCATTTTCTGA
* * * ** *
19413912 AAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTTTTAA-GATTATTAAAGGCATCTTTT
391 AAAAAAAAAAAACATTCAATAA-TTCATTTTAAAA-ATTTTTAATGATTATTAAAAACATATTTT
* * * * * *
19413976 AGTAAAA-ATGCATTCAATAATCTCGTAGTCAAATTTT-AAGGGAATTATTGAAGGTATTTTTGA
454 AGTAAAACA-ACATTCAATAATCTCATAATCAAATTTTAAAAGG-ATTATTAAAGGCATTTTTGA
* **
19414039 TCA-AAAAATGCCTTTAC-T-TAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGGTATTT
517 -CAGAAAAATGCCTTCACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGACATTT
19414101 TTTTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
581 TTTTATAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
*
19414165 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGTGTTTTTTG
1 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
* * *
19414230 -AAAAAAAAAAAAAAGCCTTCAATAATTT-CTTTTAAAATTTTTTTACGATTATTAAAGGCATCT
66 AAAAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTGTTAAGATTATTAAAGGCATCT
* *
19414293 TTTAGTAAAAATGCCTTCAATAATCTCGTAGTCAAATTTT-AAGAGAATTATTGAAGGTATTTTT
131 TTTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAG-GAATTATTGAAAGTATTTTT
* *
19414357 TATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGATGGTGAGATTATTATAGGTATT
195 GATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGATGGTGAGATTATTATAAGTATT
* *
19414422 TTTTTATAAAACGTCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
260 TTTTTATAAAACGCCTTTAATAATTCTCATAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
** *
19414487 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATGGATCGGATTATTGAAGGTATTTTCT-
325 GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAATCGGATTATTGAAGGCATTTTCTG
*
19414551 AAAAAAAAAAAACACATTCAATAATTCATTTTAAAAATTTTTAATGATTATTAAAAACGTATTTT
390 AAAAAAAAAAAA-ACATTCAATAATTCATTTTAAAAATTTTTAATGATTATTAAAAACATATTTT
* *
19414616 AGTAAAACAACTTTCAATAATCTCATAATCAAATTTTAAAAGGATTATTAAAGGCGTTTTTGACA
454 AGTAAAACAACATTCAATAATCTCATAATCAAATTTTAAAAGGATTATTAAAGGCATTTTTGACA
*
19414681 GAAAAATGCCTTCACTTATAATTTTTATATTAGTGAAGGTGGTGAGATTATTATAGACATTTTTT
519 GAAAAATGCCTTCACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGACATTTTTT
19414746 ACCAAAAACA
Statistics
Matches: 533, Mismatches: 40, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
639 9 0.02
640 103 0.19
641 288 0.54
642 71 0.13
643 62 0.12
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (644 bp):
GCATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAACCGGATTATTGAAGGCGTTTTTTG
AAAAAAAAAAAAAAAACCTTCAATAATTTCCTTTTAAAATTTTGTTAAGATTATTAAAGGCATCT
TTTAGTAAAAATACCTTCAATAATCTCGTAGTCAAATTTTAAAGGAATTATTGAAAGTATTTTTG
ATCGAAAAATGCCTTTACTTATAATTTTTATATCAGTGAAGATGGTGAGATTATTATAAGTATTT
TTTTATAAAACGCCTTTAATAATTCTCATAATATTTTTGGACTGGATTATTAAAGGCCCTTTTGG
CATAAAATGCCTCCAATAAACAAGCTATTGAAAAAATAAATCGGATTATTGAAGGCATTTTCTGA
AAAAAAAAAAAACATTCAATAATTCATTTTAAAAATTTTTAATGATTATTAAAAACATATTTTAG
TAAAACAACATTCAATAATCTCATAATCAAATTTTAAAAGGATTATTAAAGGCATTTTTGACAGA
AAAATGCCTTCACTTATAATTTTTATATCAGTGAAGGTGGTGAGATTATTATAGACATTTTTTTA
TAAAACGCCTTTAATAATTCTCGTAATATTTTTGGACTGGATTATTAAAGGCCCTTTTG
Found at i:19415605 original size:25 final size:25
Alignment explanation
Indices: 19415577--19415640 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
19415567 TTTGCTAAAG
* * *
19415577 GTTTGATGAATGGTGTTTCTGAATA
1 GTTTGCTGAATGATGGTTCTGAATA
* *
19415602 GTTTCCTGAATGATGGTTCTGAATG
1 GTTTGCTGAATGATGGTTCTGAATA
19415627 GTTTGCTGAATGAT
1 GTTTGCTGAATGAT
19415641 ATTTTGAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.08, G:0.28, T:0.42
Consensus pattern (25 bp):
GTTTGCTGAATGATGGTTCTGAATA
Found at i:19415638 original size:12 final size:12
Alignment explanation
Indices: 19415544--19415638 Score: 59
Period size: 12 Copynumber: 7.5 Consensus size: 12
19415534 ATTAGTTTAT
19415544 TGAATGGTATTGC
1 TGAATGGT-TTGC
19415557 ATGATATTGGTTTGC
1 -TGA-A-TGGTTTGC
* *
19415572 T-AAAGGTTTGA
1 TGAATGGTTTGC
*
19415583 TGAATGGTGTTTC
1 TGAATGGT-TTGC
* *
19415596 TGAATAGTTTCC
1 TGAATGGTTTGC
*
19415608 TGAATGATGGTT-C
1 TGAATG--GTTTGC
19415621 TGAATGGTTTGC
1 TGAATGGTTTGC
19415633 TGAATG
1 TGAATG
19415639 ATATTTTGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
11 10 0.16
12 21 0.33
13 17 0.27
14 7 0.11
15 5 0.08
16 4 0.06
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.41
Consensus pattern (12 bp):
TGAATGGTTTGC
Found at i:19418780 original size:35 final size:35
Alignment explanation
Indices: 19418726--19418802 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
19418716 ATATATAAAC
* *
19418726 CAAATGTTTTCTGGACATAAACCTACAATTGACTT
1 CAAATGTTTTCTGGACATAAAACTACAACTGACTT
* *
19418761 CAAATGTTTTTTGGGCATAAAACTACAACTGACTT
1 CAAATGTTTTCTGGACATAAAACTACAACTGACTT
*
19418796 CACATGT
1 CAAATGT
19418803 ATAATTAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (35 bp):
CAAATGTTTTCTGGACATAAAACTACAACTGACTT
Found at i:19418974 original size:17 final size:18
Alignment explanation
Indices: 19418947--19418990 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
19418937 AAATTTATTA
19418947 AATGCTTTTTTGACAAAG
1 AATGCTTTTTTGACAAAG
*
19418965 AATGTTTTTTTGACAAA-
1 AATGCTTTTTTGACAAAG
19418982 AATTGCTTT
1 AA-TGCTTT
19418991 CAATAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (18 bp):
AATGCTTTTTTGACAAAG
Found at i:19419301 original size:59 final size:59
Alignment explanation
Indices: 19419184--19419301 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
19419174 CCCCCAAATT
* * * * * **
19419184 TTTTGTTTGGAGTATTGAAGGCGTATTTGGGCAGAAAACGTCTTCAATCATCTTTTAGA
1 TTTTGTATGAAGTATTGAAAGCGTATTTGGACAGAAAACGCCTTCAATCATCCCTTAGA
* *
19419243 TTTTGTATGAAGTATTGAAAGTGTATTTGGACAGAAAATGCCTTCAATCATCCCTTAGA
1 TTTTGTATGAAGTATTGAAAGCGTATTTGGACAGAAAACGCCTTCAATCATCCCTTAGA
19419302 AATAATCCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (59 bp):
TTTTGTATGAAGTATTGAAAGCGTATTTGGACAGAAAACGCCTTCAATCATCCCTTAGA
Found at i:19422871 original size:12 final size:12
Alignment explanation
Indices: 19422854--19422888 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
19422844 TTCCAAGTGA
19422854 AAGTGAGAATCC
1 AAGTGAGAATCC
19422866 AAGTGAGAATCC
1 AAGTGAGAATCC
19422878 AAGTGAGAATC
1 AAGTGAGAATC
19422889 AACAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (12 bp):
AAGTGAGAATCC
Found at i:19424939 original size:13 final size:13
Alignment explanation
Indices: 19424921--19424946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19424911 CCTCCTTCCC
19424921 CAACATTGTGTAT
1 CAACATTGTGTAT
19424934 CAACATTGTGTAT
1 CAACATTGTGTAT
19424947 GTATTTTCAG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CAACATTGTGTAT
Found at i:19426436 original size:21 final size:21
Alignment explanation
Indices: 19426410--19426451 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19426400 AATTCCTAAC
**
19426410 TTATCAGCATTCGATAGGTCT
1 TTATCAGCATTAAATAGGTCT
*
19426431 TTATCAGTATTAAATAGGTCT
1 TTATCAGCATTAAATAGGTCT
19426452 GAAAGGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (21 bp):
TTATCAGCATTAAATAGGTCT
Found at i:19426568 original size:16 final size:16
Alignment explanation
Indices: 19426547--19426591 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
19426537 TAATTCAAGT
19426547 TTTAAATTTTAATAAA
1 TTTAAATTTTAATAAA
* *
19426563 TTTAAATCTTAATTAA
1 TTTAAATTTTAATAAA
* *
19426579 TTTGAGTTTTAAT
1 TTTAAATTTTAAT
19426592 TCAAGTTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
TTTAAATTTTAATAAA
Found at i:19433025 original size:53 final size:53
Alignment explanation
Indices: 19432944--19433048 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
19432934 TGGGGCCAGA
* *
19432944 AACATTGCCTTTGCTTAACTTAGGTGACAGTTTCATCTTCACTTTGATCCTTC
1 AACATTACCTTTGCTTAACTTAGATGACAGTTTCATCTTCACTTTGATCCTTC
*
19432997 AACATTACCTTTGCTTAGCTTAGATGACAGTTTCATCTTCACTTTGATCCTT
1 AACATTACCTTTGCTTAACTTAGATGACAGTTTCATCTTCACTTTGATCCTT
19433049 TCTTTTGATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (53 bp):
AACATTACCTTTGCTTAACTTAGATGACAGTTTCATCTTCACTTTGATCCTTC
Found at i:19436988 original size:17 final size:17
Alignment explanation
Indices: 19436968--19437001 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19436958 TCACAGTAAG
19436968 ACTTTCCAAGCATTTCA
1 ACTTTCCAAGCATTTCA
19436985 ACTTTCCAAGCATTTCA
1 ACTTTCCAAGCATTTCA
19437002 TTATTTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
ACTTTCCAAGCATTTCA
Found at i:19442645 original size:20 final size:20
Alignment explanation
Indices: 19442608--19442646 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19442598 TGTTTTTTTT
* *
19442608 TCCTTCAAATTTTTAATCTA
1 TCCTTCAAATCTTCAATCTA
*
19442628 TCCTTTAAATCTTCAATCT
1 TCCTTCAAATCTTCAATCT
19442647 CTATGAACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (20 bp):
TCCTTCAAATCTTCAATCTA
Found at i:19444674 original size:23 final size:23
Alignment explanation
Indices: 19444619--19444674 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
19444609 TTTTTATAAA
*
19444619 AAAATCATAAAATAACAAATTTT
1 AAAATCATTAAATAACAAATTTT
* **
19444642 AAATAT-ATTAAATATCATTTTTT
1 AAA-ATCATTAAATAACAAATTTT
19444665 AAAATCATTA
1 AAAATCATTA
19444675 TATGCATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATCATTAAATAACAAATTTT
Found at i:19444787 original size:2 final size:2
Alignment explanation
Indices: 19444780--19444806 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19444770 AGGAGATGGG
19444780 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 T
19444807 TGAATTAGAT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19446066 original size:12 final size:12
Alignment explanation
Indices: 19446049--19446073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19446039 TCGCTTTGAA
19446049 TTTTTATTAAAT
1 TTTTTATTAAAT
19446061 TTTTTATTAAAT
1 TTTTTATTAAAT
19446073 T
1 T
19446074 ATTTGTAATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTATTAAAT
Found at i:19454125 original size:25 final size:25
Alignment explanation
Indices: 19454074--19454135 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
19454064 CTTAGATCAA
* *
19454074 AATAGTAAAA-TTAAATTTTTTATT
1 AATAATAAAATTTAAATTTTTTACT
**
19454098 AATTTTAAAATTTATAATTTTTT-CT
1 AATAATAAAATTTA-AATTTTTTACT
19454123 AATAATAAAATTT
1 AATAATAAAATTT
19454136 TTCATTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 8 0.26
25 15 0.48
26 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
AATAATAAAATTTAAATTTTTTACT
Found at i:19463457 original size:12 final size:13
Alignment explanation
Indices: 19463428--19463457 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19463418 TCAACCAAAA
*
19463428 AAAAATATTTTAT
1 AAAAACATTTTAT
19463441 AAAAACATTTTAT
1 AAAAACATTTTAT
19463454 AAAA
1 AAAA
19463458 TGTCAAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAACATTTTAT
Found at i:19465130 original size:18 final size:20
Alignment explanation
Indices: 19465103--19465147 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19465093 TATGTATATG
19465103 ATATAAATAT-TAA-ATTTT
1 ATATAAATATATAATATTTT
*
19465121 ATATATATATATAATATTTT
1 ATATAAATATATAATATTTT
19465141 ATATAAA
1 ATATAAA
19465148 AATTATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATAAATATATAATATTTT
Found at i:19465155 original size:18 final size:18
Alignment explanation
Indices: 19465103--19465161 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
19465093 TATGTATATG
*
19465103 ATATAAATATTAAATTTT
1 ATATAAATATTATATTTT
*
19465121 ATATATATATATAATATTTT
1 ATATA-A-ATATTATATTTT
* *
19465141 ATATAAAAATTATATGTT
1 ATATAAATATTATATTTT
19465159 ATA
1 ATA
19465162 ATTTATATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 17 0.50
19 2 0.06
20 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATAAATATTATATTTT
Found at i:19465986 original size:2 final size:2
Alignment explanation
Indices: 19465979--19466009 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19465969 GTTTCCTTTG
19465979 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19466010 TTTTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19466059 original size:24 final size:23
Alignment explanation
Indices: 19466024--19466068 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
19466014 ATTATTTATT
*
19466024 TAATTTTATATTTATATTTTAAAA
1 TAATTTTATATTAAT-TTTTAAAA
19466048 TAATATTT-TATTAATTTTTAA
1 TAAT-TTTATATTAATTTTTAA
19466069 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 10 0.53
25 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATTTTATATTAATTTTTAAAA
Found at i:19466118 original size:40 final size:40
Alignment explanation
Indices: 19466044--19466122 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
19466034 TTTATATTTT
* * *
19466044 AAAATAATATTTTATTAATTTTTAATTAAATTAAATATTA
1 AAAATAATATTTTATTAAATTTAAATGAAATTAAATATTA
**
19466084 AAAATAATATTTTATTAAATTTAAATGATTTTAAATATT
1 AAAATAATATTTTATTAAATTTAAATGAAATTAAATATT
19466123 TATTATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
AAAATAATATTTTATTAAATTTAAATGAAATTAAATATTA
Found at i:19470432 original size:18 final size:18
Alignment explanation
Indices: 19470409--19470455 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
19470399 AAAATGGTAT
19470409 TATTTTATATTTAATAAA
1 TATTTTATATTTAATAAA
* *
19470427 TATTTTAT-TTT-TTATA
1 TATTTTATATTTAATAAA
19470443 -ATTTTATATTTAA
1 TATTTTATATTTAA
19470456 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 3 0.12
18 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATATTTAATAAA
Found at i:19470475 original size:33 final size:33
Alignment explanation
Indices: 19470410--19470477 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19470400 AAATGGTATT
**
19470410 ATTTTATATTTAATAAATATTTTATTTTTTATA
1 ATTTTATATTTAATAAATATTTTATTACTTATA
19470443 ATTTTATATTTAAATTAAA-ATTTT-TTACTTATA
1 ATTTTATATTT-AA-TAAATATTTTATTACTTATA
19470476 AT
1 AT
19470478 CAATAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 20 0.65
34 7 0.23
35 4 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (33 bp):
ATTTTATATTTAATAAATATTTTATTACTTATA
Found at i:19471011 original size:24 final size:23
Alignment explanation
Indices: 19470956--19471012 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
19470946 GATTTAAAAA
19470956 AATTAAAAAAATTATTTAATTAT
1 AATTAAAAAAATTATTTAATTAT
* *
19470979 GATCAAAAAAATTATTATAATTAT
1 AATTAAAAAAATTATT-TAATTAT
*
19471003 AATTTAAAAA
1 AATTAAAAAA
19471013 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AATTAAAAAAATTATTTAATTAT
Found at i:19471026 original size:26 final size:26
Alignment explanation
Indices: 19470997--19471062 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
19470987 AAATTATTAT
19470997 AATTATA-ATTTAAAAATTTTAATAAA
1 AATTATATATTTAAAAATTTT-ATAAA
* *
19471023 AATT-TATATTAAATAAATTTTATTAA
1 AATTATATATTTAA-AAATTTTATAAA
19471049 AATTA-ATATTTAAA
1 AATTATATATTTAAA
19471063 TTTAATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 3 0.09
26 24 0.71
27 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTATATATTTAAAAATTTTATAAA
Found at i:19471040 original size:27 final size:27
Alignment explanation
Indices: 19471010--19471063 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
19471000 TATAATTTAA
*
19471010 AAATTTTAATAAAAATTTATA-TTAAAT
1 AAATTTT-ATAAAAATTAATATTTAAAT
*
19471037 AAATTTTATTAAAATTAATATTTAAAT
1 AAATTTTATAAAAATTAATATTTAAAT
19471064 TTAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTTTATAAAAATTAATATTTAAAT
Found at i:19471264 original size:28 final size:25
Alignment explanation
Indices: 19471210--19471260 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
19471200 TTTGGATGAT
19471210 ATTTAAAAATTAAAATATTATTTTA
1 ATTTAAAAATTAAAATATTATTTTA
19471235 ATTTAAACTAATTATAAAT-TTATTTT
1 ATTTAAA--AATTA-AAATATTATTTT
19471261 TAATCAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTAAAAATTAAAATATTATTTTA
Found at i:19474332 original size:14 final size:14
Alignment explanation
Indices: 19474313--19474342 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19474303 GCAAGGTAAG
19474313 ACTCTATGAAAGGA
1 ACTCTATGAAAGGA
19474327 ACTCTATGAAAGGA
1 ACTCTATGAAAGGA
19474341 AC
1 AC
19474343 AAGTTTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (14 bp):
ACTCTATGAAAGGA
Found at i:19489842 original size:25 final size:24
Alignment explanation
Indices: 19489792--19489842 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
19489782 GATGAGATTA
* *
19489792 AAATTAATAATAAAATATATATTT
1 AAATTAAAAATAAAATATATAGTT
19489816 AAATGTAAAAATAAAA-ATGATAGTT
1 AAAT-TAAAAATAAAATAT-ATAGTT
19489841 AA
1 AA
19489843 GAACATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATTAAAAATAAAATATATAGTT
Found at i:19490696 original size:2 final size:2
Alignment explanation
Indices: 19490685--19490714 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19490675 TCTTTCTTTT
19490685 TA TA -A 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 T
19490715 TGGTAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19500549 original size:15 final size:15
Alignment explanation
Indices: 19500531--19500566 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
19500521 TTAATTTTTC
19500531 TATATATTATTTTAA
1 TATATATTATTTTAA
19500546 TATATA-T-TTTTAA
1 TATATATTATTTTAA
19500559 TATA-ATTA
1 TATATATTA
19500567 AATAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.05
13 11 0.58
14 1 0.05
15 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATATTATTTTAA
Found at i:19506044 original size:30 final size:30
Alignment explanation
Indices: 19505994--19506160 Score: 153
Period size: 29 Copynumber: 5.6 Consensus size: 30
19505984 AATGCATAGT
*
19505994 GACTAAATTCCTTAAAAAATAATACTATAGG
1 GACTAAATTCCTT-AAAAATAATACTACAGG
* * * *
19506025 GATTAAATTTCTTAAAAATAATATTACAAG
1 GACTAAATTCCTTAAAAATAATACTACAGG
* * * *
19506055 GACTAAATTCCTT-TAAATATTACTAAAGC
1 GACTAAATTCCTTAAAAATAATACTACAGG
* * *
19506084 GACTAAATTTCTTAAAAATAATATTACAAG
1 GACTAAATTCCTTAAAAATAATACTACAGG
* **
19506114 GA-TAAAATTCCTT-TAAATAATACTATGGG
1 GACT-AAATTCCTTAAAAATAATACTACAGG
19506143 GACTAAATTCC-TAAAAAT
1 GACTAAATTCCTTAAAAAT
19506161 CGAAAAGTAC
Statistics
Matches: 105, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.01
29 47 0.45
30 46 0.44
31 11 0.10
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (30 bp):
GACTAAATTCCTTAAAAATAATACTACAGG
Found at i:19506087 original size:29 final size:28
Alignment explanation
Indices: 19505994--19506154 Score: 117
Period size: 30 Copynumber: 5.4 Consensus size: 28
19505984 AATGCATAGT
* *
19505994 GACTAAATTCCTTAAAAAATAATACTATAGG
1 GACTAAATTCCTT--TAAATAATACTA-AAG
* * * *
19506025 GATTAAATTTCTTAAAAATAATATTACAAG
1 GACTAAATTCCTT-TAAATAATACTA-AAG
*
19506055 GACTAAATTCCTTTAAATATTACTAAAG
1 GACTAAATTCCTTTAAATAATACTAAAG
* * *
19506083 CGACTAAATTTCTTAAAAATAATATTACAAG
1 -GACTAAATTCCTT-TAAATAATACTA-AAG
**
19506114 GA-TAAAATTCCTTTAAATAATACTATGGG
1 GACT-AAATTCCTTTAAATAATACTA-AAG
19506143 GACTAAATTCCT
1 GACTAAATTCCT
19506155 AAAAATCGAA
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
28 3 0.03
29 43 0.41
30 45 0.43
31 14 0.13
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (28 bp):
GACTAAATTCCTTTAAATAATACTAAAG
Found at i:19506091 original size:59 final size:59
Alignment explanation
Indices: 19505994--19506160 Score: 230
Period size: 59 Copynumber: 2.8 Consensus size: 59
19505984 AATGCATAGT
* *
19505994 GACTAAATTCCTTAAAAAATAATACTATAGGGATTAAATTTCTTAAAAATAATATTACAAG
1 GACTAAATTCCTT--TAAATAATACTATAGGGACTAAATTTCTTAAAAATAATATTACAAG
* * *
19506055 GACTAAATTCCTTTAAATATTACTAAAGCGACTAAATTTCTTAAAAATAATATTACAAG
1 GACTAAATTCCTTTAAATAATACTATAGGGACTAAATTTCTTAAAAATAATATTACAAG
* *
19506114 GA-TAAAATTCCTTTAAATAATACTATGGGGACTAAA-TTCCTAAAAAT
1 GACT-AAATTCCTTTAAATAATACTATAGGGACTAAATTTCTTAAAAAT
19506161 CGAAAAGTAC
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
58 11 0.12
59 71 0.75
61 13 0.14
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (59 bp):
GACTAAATTCCTTTAAATAATACTATAGGGACTAAATTTCTTAAAAATAATATTACAAG
Found at i:19510496 original size:18 final size:18
Alignment explanation
Indices: 19510466--19510503 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
19510456 TTTATAATAA
*
19510466 AAAATATTTTATTTT-TT
1 AAAATATTATATTTTATT
19510483 AAAATATTAATATTTTATT
1 AAAATATT-ATATTTTATT
19510502 AA
1 AA
19510504 CTTCAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAAATATTATATTTTATT
Found at i:19514217 original size:25 final size:25
Alignment explanation
Indices: 19514183--19514236 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19514173 CATTAAAATT
*
19514183 TTTTTTCAATCA-TAGCTACAATAAC
1 TTTTTTCAAT-AGCAGCTACAATAAC
*
19514208 TTTTTTCAATAGCAGCTACAGTAAC
1 TTTTTTCAATAGCAGCTACAATAAC
19514233 TTTT
1 TTTT
19514237 ATTACTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (25 bp):
TTTTTTCAATAGCAGCTACAATAAC
Found at i:19532475 original size:27 final size:27
Alignment explanation
Indices: 19532434--19532490 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
19532424 ACTTGTCAAT
19532434 TTCCCAACCAACCCCTTCAAAACCAGA
1 TTCCCAACCAACCCCTTCAAAACCAGA
* * *
19532461 TTCCCAACCAGCCCCTTCAACACTAGA
1 TTCCCAACCAACCCCTTCAAAACCAGA
19532488 TTC
1 TTC
19532491 TCAAACTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.44, G:0.05, T:0.19
Consensus pattern (27 bp):
TTCCCAACCAACCCCTTCAAAACCAGA
Found at i:19535408 original size:39 final size:39
Alignment explanation
Indices: 19535363--19535439 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
19535353 ATACTTCTCA
*
19535363 AACTCCCTTTCACGTCCAAAACATCCAACCAAATCCTCT
1 AACTCCCTTTCAAGTCCAAAACATCCAACCAAATCCTCT
* *
19535402 AACTCCCTTTCAAGTGCATAACATCCAACCAAATCCTC
1 AACTCCCTTTCAAGTCCAAAACATCCAACCAAATCCTC
19535440 CAATCTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.34, C:0.39, G:0.04, T:0.23
Consensus pattern (39 bp):
AACTCCCTTTCAAGTCCAAAACATCCAACCAAATCCTCT
Found at i:19550472 original size:2 final size:2
Alignment explanation
Indices: 19550429--19550456 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19550419 AGTATACCAT
19550429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19550457 CACACATTCA
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):
TA
Found at i:19550680 original size:16 final size:16
Alignment explanation
Indices: 19550655--19550695 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
19550645 TCCTATTTAT
*
19550655 ATACATACATACATAC
1 ATACACACATACATAC
* *
19550671 ATACACACATATATAT
1 ATACACACATACATAC
19550687 ATACACACA
1 ATACACACA
19550696 CACAACCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
ATACACACATACATAC
Found at i:19550690 original size:20 final size:20
Alignment explanation
Indices: 19550657--19550699 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19550647 CTATTTATAT
*
19550657 ACATACATACATACATACAC
1 ACATACATACATACACACAC
* *
19550677 ACATATATATATACACACAC
1 ACATACATACATACACACAC
19550697 ACA
1 ACA
19550700 ACCAATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (20 bp):
ACATACATACATACACACAC
Found at i:19555733 original size:3 final size:3
Alignment explanation
Indices: 19555727--19555756 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19555717 TTTTTTTAAA
19555727 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19555757 GACTTAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19557310 original size:64 final size:64
Alignment explanation
Indices: 19557186--19557310 Score: 146
Period size: 64 Copynumber: 2.0 Consensus size: 64
19557176 GCATTTAGAG
* * * * *
19557186 TTTTTATTTTAAGAAAAATTAATACTTTCAACTTTTTCCTCAAAATATTTTTTTTATTTTGAAA
1 TTTTAATTTTAAGAAAAATTAATACTTTCAACTTTTTCCTAAAAAAAATATTTTTATTTTGAAA
* * *
19557250 TTTTAATTTTGAA-AAAAATTGATACTTTTAACTTTTTCTTAAAACAAAATATTTTT-TTTTG
1 TTTTAATTTT-AAGAAAAATTAATACTTTCAACTTTTTCCTAAAA-AAAATATTTTTATTTTG
19557311 TTCAAAGGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
64 41 0.80
65 10 0.20
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (64 bp):
TTTTAATTTTAAGAAAAATTAATACTTTCAACTTTTTCCTAAAAAAAATATTTTTATTTTGAAA
Found at i:19557484 original size:5 final size:6
Alignment explanation
Indices: 19557463--19557505 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
19557453 AAGAAAGAAA
* *
19557463 AAAATT AAAATT AAAA-T AAAATT AAGATT AAGATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AA
19557506 GGAATACCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:19557549 original size:5 final size:5
Alignment explanation
Indices: 19557530--19557562 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
19557520 TCCTAAATTA
19557530 AAAAT AATAAT -AAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAA
19557563 CTTTGAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:19558393 original size:14 final size:14
Alignment explanation
Indices: 19558376--19558507 Score: 59
Period size: 13 Copynumber: 9.6 Consensus size: 14
19558366 TGATTAAGAA
19558376 AAAAAGATAAA-AAT
1 AAAAA-ATAAATAAT
19558390 AAAAAATAAATAAT
1 AAAAAATAAATAAT
*
19558404 ---AGATAAATAAT
1 AAAAAATAAATAAT
* *
19558415 AAAATAT-ATTAAT
1 AAAAAATAAATAAT
*
19558428 AGAAAAGTAAA-AA-
1 A-AAAAATAAATAAT
19558441 AAAATAGATAAATAA-
1 AAAA-A-ATAAATAAT
* *
19558456 AAAATATTAATAGAT
1 AAAAAATAAATA-AT
19558471 AAAAAAT-AATAAT
1 AAAAAATAAATAAT
*
19558484 AATCATAAT-AATAAT
1 AA--AAAATAAATAAT
*
19558499 GAAAAATAA
1 AAAAAATAA
19558508 TAAAATTAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
11 10 0.11
12 3 0.03
13 27 0.30
14 27 0.30
15 24 0.26
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (14 bp):
AAAAAATAAATAAT
Found at i:19558483 original size:17 final size:17
Alignment explanation
Indices: 19558376--19558485 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 17
19558366 TGATTAAGAA
*
19558376 AAAAAGATAAAAATAAA-
1 AAAAA-ATAATAATAAAT
19558393 AAATAAATAATAGATAAAT
1 AAA-AAATAATA-ATAAAT
19558412 AATAAAATATATTAATAGAAAAGT
1 AA-AAAATA-A-TAAT---AAA-T
*
19558436 AAAAAAAAATAGATAAAT
1 AAAAAATAATA-ATAAAT
* *
19558454 AAAAAATATTAATAGAT
1 AAAAAATAATAATAAAT
19558471 AAAAAATAATAATAA
1 AAAAAATAATAATAA
19558486 TCATAATAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
17 26 0.35
18 17 0.23
19 10 0.13
20 4 0.05
21 4 0.05
22 3 0.04
23 8 0.11
24 3 0.04
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAAAATAATAATAAAT
Found at i:19558494 original size:39 final size:39
Alignment explanation
Indices: 19558388--19558494 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 39
19558378 AAAGATAAAA
*
19558388 ATAAAAAATAAATAATAGATAAATAATAAAATATATTAATAG
1 ATAAAAAAT-AATAATAGAT--ATAATAAAAAATATTAATAG
* *
19558430 A-AAAGTAAAAAAAAATAGATA-AATAAAAAATATTAATAG
1 ATAAA--AAATAATAATAGATATAATAAAAAATATTAATAG
19558469 ATAAAAAATAATAATA-ATCATAATAA
1 ATAAAAAATAATAATAGAT-ATAATAA
19558495 TAATGAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
37 2 0.04
38 10 0.18
39 23 0.42
40 4 0.07
41 3 0.05
42 10 0.18
43 3 0.05
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (39 bp):
ATAAAAAATAATAATAGATATAATAAAAAATATTAATAG
Found at i:19558504 original size:63 final size:62
Alignment explanation
Indices: 19558373--19558525 Score: 161
Period size: 63 Copynumber: 2.4 Consensus size: 62
19558363 AATTGATTAA
*
19558373 GAAAAAAAGATAAAAATAAAAAATAAATAATAGATAAATAATAAAATATATTAATAGAAAAGT
1 GAAAAAAA-ATAAAAATAAAAAATAAATAATAGATAAAAAATAAAATATATTAATAGAAAAGT
* * *
19558436 AAAAAAAAATAGATAAATAAAAAAT-ATTAATAGATAAAAAATAATAATA-ATCATAATA-ATAA
1 GAAAAAAAATA-A-AAATAAAAAATAAATAATAGATAAAAAATAA-AATATAT--TAATAGAAAA
19558498 -T
61 GT
* * *
19558499 GAAAAATAATAAAATTAAAAATTAAAT
1 GAAAAAAAATAAAAATAAAAAATAAAT
19558526 TAAATTAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
61 9 0.12
62 6 0.08
63 37 0.49
64 18 0.24
65 5 0.07
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (62 bp):
GAAAAAAAATAAAAATAAAAAATAAATAATAGATAAAAAATAAAATATATTAATAGAAAAGT
Found at i:19558527 original size:5 final size:5
Alignment explanation
Indices: 19558517--19558544 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
19558507 ATAAAATTAA
19558517 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
19558545 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:19558805 original size:45 final size:44
Alignment explanation
Indices: 19558746--19558966 Score: 171
Period size: 45 Copynumber: 5.0 Consensus size: 44
19558736 AAATTTTGAT
* * *
19558746 CAAAGCTCTTTTAAGTAGAGGCTCAATGA-TTTTGAGTAAAATAAA
1 CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGA--AAAATAAA
19558791 CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGAAAAATAAA
1 CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGAAAAATAAA
* * * * * * *
19558835 TAAAGCTCCTCTAAACATATGCTCAAAGACTTTT-AGAAAGT-AA
1 CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGA-AAAATAAA
** * * * ** *
19558878 -ATTGCTCCTCTAAACAGAGGCTCCATAACTTTTAAAGAAATAAA
1 CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGAA-AAATAAA
* * * *
19558922 CAAAGCTCCTTTAAGCAGAGGTTTAACAAATTTTGAAGAAATAAA
1 CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGAA-AAATAAA
19558967 TAACTCCTCT
Statistics
Matches: 142, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
42 27 0.19
43 7 0.05
44 42 0.30
45 60 0.42
46 6 0.04
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (44 bp):
CAAAGCTCCTTTAAGCAGAGGCTCAACGACTTTTGAAAAATAAA
Found at i:19558843 original size:44 final size:44
Alignment explanation
Indices: 19558762--19559173 Score: 197
Period size: 41 Copynumber: 9.7 Consensus size: 44
19558752 TCTTTTAAGT
* * * *
19558762 AGAGGCTCAATGA-TTTTGAGTAAAATAAACAAAGCTCCTTTAAGC
1 AGAGGCTCAACGACTTTTGA--AAAATAAATAAAGCTCCTCTAAAC
19558807 AGAGGCTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAAC
1 AGAGGCTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAAC
* * * * *
19558851 ATATGCTCAAAGACTTTT-AGAAAGTAAAT--TGCTCCTCTAAAC
1 AGAGGCTCAACGACTTTTGA-AAAATAAATAAAGCTCCTCTAAAC
* ** * * * *
19558893 AGAGGCTCCATAACTTTTAAAGAAATAAACAAAGCTCCTTTAAGC
1 AGAGGCTCAACGACTTTTGAA-AAATAAATAAAGCTCCTCTAAAC
* * * *
19558938 AGAGGTTTAACAAATTTTGAAGAAATAAAT-AA-CTCCTCTAAAC
1 AGAGGCTCAACGACTTTTGAA-AAATAAATAAAGCTCCTCTAAAC
* * * * * *
19558981 AGAGG-T-ATCGCAACTTTTG-ATAGTAAAT--TGCTCATCTAAGC
1 AGAGGCTCAACG--ACTTTTGAAAAATAAATAAAGCTCCTCTAAAC
* * * * * *
19559022 AGAGGCACCACAAC-TTTGGAAAATAAAT--TGCTTCTCTAAAC
1 AGAGGCTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAAC
* * *
19559063 AGAGGCTTAACAAC--TT-AAAAATAAATAAATAACTCCTCTAAAC
1 AGAGGCTCAACGACTTTTGAAAAATAAAT-AA-AGCTCCTCTAAAC
* *
19559106 AGAGG--CAACGAAC-TTTGAGAAATAAAT--TGCTCCTCTAAAC
1 AGAGGCTCAACG-ACTTTTGAAAAATAAATAAAGCTCCTCTAAAC
* * *
19559146 AGATGCACCAA-AAC-TTTGAAAAATAAAT
1 AGAGGC-TCAACGACTTTTGAAAAATAAAT
19559174 GGCTCATCAA
Statistics
Matches: 285, Mismatches: 60, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
39 9 0.03
40 21 0.07
41 70 0.25
42 30 0.11
43 49 0.17
44 55 0.19
45 45 0.16
46 6 0.02
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (44 bp):
AGAGGCTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAAC
Found at i:19559161 original size:83 final size:85
Alignment explanation
Indices: 19559015--19559173 Score: 202
Period size: 83 Copynumber: 1.9 Consensus size: 85
19559005 AAATTGCTCA
* * **
19559015 TCTAAGCAGAGGCACCACAACTTTGGAAAATAAATTGCTTCTCTAAACAGAGGCTTAACAAC-TT
1 TCTAAACAGAGGCA-CACAACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCCCAACAACTTT
19559079 -AAAAATAAATAAATAACTCC
65 GAAAAATAAATAAATAACTCC
*
19559099 TCTAAACAGAGGCA-ACGAACTTT-GAGAAATAAATTGCTCCTCTAAACAGATGCACCAA-AACT
1 TCTAAACAGAGGCACAC-AACTTTGGA-AAATAAATTGCTCCTCTAAACAGAGGC-CCAACAACT
19559161 TTGAAAAATAAAT
63 TTGAAAAATAAAT
19559174 GGCTCATCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
82 4 0.06
83 34 0.52
84 17 0.26
85 10 0.15
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (85 bp):
TCTAAACAGAGGCACACAACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCCCAACAACTTTG
AAAAATAAATAAATAACTCC
Found at i:19559449 original size:16 final size:16
Alignment explanation
Indices: 19559428--19559469 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
19559418 ATATGCTATG
*
19559428 CAATGCGTGCGAAATT
1 CAATGCATGCGAAATT
*
19559444 CAATGCATGTGAAATT
1 CAATGCATGCGAAATT
19559460 CAATGCATGC
1 CAATGCATGC
19559470 TATGCAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (16 bp):
CAATGCATGCGAAATT
Found at i:19560190 original size:10 final size:10
Alignment explanation
Indices: 19560175--19560199 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19560165 TTTCATTCCC
19560175 TTTTTTTCTT
1 TTTTTTTCTT
19560185 TTTTTTTCTT
1 TTTTTTTCTT
19560195 TTTTT
1 TTTTT
19560200 AAGCATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:19571521 original size:22 final size:21
Alignment explanation
Indices: 19571495--19571541 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19571485 AAATTCCTAG
*
19571495 AAAAAAATAACCAAAAATTTTT
1 AAAAAAAT-ACCAAAAATCTTT
* *
19571517 AAAAAAATTCCTAAAATCTTT
1 AAAAAAATACCAAAAATCTTT
19571538 AAAA
1 AAAA
19571542 TTGCTTCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAAATACCAAAAATCTTT
Found at i:19571831 original size:3 final size:3
Alignment explanation
Indices: 19571802--19571921 Score: 70
Period size: 3 Copynumber: 39.3 Consensus size: 3
19571792 GAAAAAAAAG
* *
19571802 ATA AAA ATA A-A A-A ATA ATA GATAA ATA ATA A-A AT- ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA
* * * * *
19571845 GATA ACTA A-A AAA ATA TTA ATA GATAA ATA ATA ATA ATC ATT ATC ATA
1 -ATA A-TA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA
*
19571893 ATA ATA ATA ATA ATA ATGA AAA ATA ATA A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA A
19571922 AATTAAATTA
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
2 10 0.11
3 65 0.70
4 16 0.17
5 2 0.02
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:19571861 original size:22 final size:24
Alignment explanation
Indices: 19571800--19571878 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 24
19571790 AAGAAAAAAA
19571800 AGATAAA-AATAAAA-A-A-TAAT
1 AGATAAATAATAAAATATATTAAT
19571820 AGATAAATAATAAAATATATTAAT
1 AGATAAATAATAAAATATATTAAT
*
19571844 AGATAACTAA-AAAA-ATATTAAT
1 AGATAAATAATAAAATATATTAAT
19571866 AGATAAATAATAA
1 AGATAAATAATAA
19571879 TAATCATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
20 7 0.13
21 7 0.13
22 18 0.35
23 7 0.13
24 13 0.25
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (24 bp):
AGATAAATAATAAAATATATTAAT
Found at i:19571879 original size:14 final size:14
Alignment explanation
Indices: 19571808--19571880 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 14
19571798 AAAGATAAAA
*
19571808 ATAAAAAATAATAG
1 ATAAATAATAATAG
*
19571822 ATAAATAATAAAATAT
1 ATAAATAAT--AATAG
* *
19571838 ATTAATAGATAACTAA
1 ATAAATA-ATAA-TAG
* *
19571854 AAAAATATTAATAG
1 ATAAATAATAATAG
19571868 ATAAATAATAATA
1 ATAAATAATAATA
19571881 ATCATTATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
14 21 0.47
15 5 0.11
16 17 0.38
17 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (14 bp):
ATAAATAATAATAG
Found at i:19571928 original size:6 final size:6
Alignment explanation
Indices: 19571919--19571951 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
19571909 TGAAAAATAA
19571919 TAAAAT T-AAAT T-AAAT TAAAAT TAAAAT TAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAA
19571952 AAATGTGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAAAT
Found at i:19572756 original size:13 final size:13
Alignment explanation
Indices: 19572738--19572771 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19572728 GGACTATGAT
19572738 GGTTTGGTGAAGG
1 GGTTTGGTGAAGG
*
19572751 GGTTTGGTGATGG
1 GGTTTGGTGAAGG
*
19572764 GGCTTGGT
1 GGTTTGGT
19572772 AAAAGGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.03, G:0.53, T:0.35
Consensus pattern (13 bp):
GGTTTGGTGAAGG
Done.