Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 19 of 20
Found at i:8158484 original size:14 final size:14
Alignment explanation
Indices: 8158465--8158493 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8158455 ATTTATATTA
8158465 ATAGTGATGTAAGC
1 ATAGTGATGTAAGC
8158479 ATAGTGATGTAAGC
1 ATAGTGATGTAAGC
8158493 A
1 A
8158494 ATTATGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (14 bp):
ATAGTGATGTAAGC
Found at i:8168373 original size:149 final size:149
Alignment explanation
Indices: 8168117--8168393 Score: 428
Period size: 149 Copynumber: 1.9 Consensus size: 149
8168107 TTGGTAAACT
* * * * * *
8168117 TTGGCACATAGGACTTGGTTGAAGGAAGGGTTAGTACAACTAAATAGTTTCCTATGTGAGTTAGG
1 TTGGCACACAAGACTTGGTTGAAGGAAGGGTTACTACAACTAAACAGTTACCTATGCGAGTTAGG
* *
8168182 ACGAAATATTTTGATAATATGATGGTTTTCATCTTGATTATTTTTATTGCAGCCTCATATCTTGG
66 ACGAAATATTCTAATAATATGATGGTTTTCATCTTGATTATTTTTATTGCAGCCTCATATCTTGG
8168247 GTTAGGTGTTATGTAAAGA
131 GTTAGGTGTTATGTAAAGA
*
8168266 TTGGCACACAAGACTTGGTTGAAGGAAGGGTTACTACAGCTAAACAGTTACCTATGCGAGTTAGG
1 TTGGCACACAAGACTTGGTTGAAGGAAGGGTTACTACAACTAAACAGTTACCTATGCGAGTTAGG
** * * *
8168331 ATTAAATATTCTAATAATGTGATGGTTTTCATCTTGATTATTTTTATTGTAGCCTCATCTCTT
66 ACGAAATATTCTAATAATATGATGGTTTTCATCTTGATTATTTTTATTGCAGCCTCATATCTT
8168394 ACTTGGGTTG
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
149 114 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (149 bp):
TTGGCACACAAGACTTGGTTGAAGGAAGGGTTACTACAACTAAACAGTTACCTATGCGAGTTAGG
ACGAAATATTCTAATAATATGATGGTTTTCATCTTGATTATTTTTATTGCAGCCTCATATCTTGG
GTTAGGTGTTATGTAAAGA
Found at i:8173587 original size:15 final size:15
Alignment explanation
Indices: 8173567--8173608 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
8173557 CAATTGATGA
8173567 TTTGTTATTTTTGTT-
1 TTTGTTATTTTT-TTC
8173582 TTTGTT-TTTTTTTC
1 TTTGTTATTTTTTTC
*
8173596 TTTTTTATTTTTT
1 TTTGTTATTTTTT
8173609 ACAAACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 12 0.50
ACGTcount: A:0.05, C:0.02, G:0.07, T:0.86
Consensus pattern (15 bp):
TTTGTTATTTTTTTC
Found at i:8181768 original size:221 final size:220
Alignment explanation
Indices: 8181368--8181807 Score: 828
Period size: 221 Copynumber: 2.0 Consensus size: 220
8181358 AAATAAGTGC
8181368 CGATTCACGCGTTAAGAAAATTGACTTTACCCCTACCAATGTGTTTTTGTTCATCTCACCCCCAA
1 CGATTCACGCGTTAAGAAAATTGACTTTACCCCTACCAATGTGTTTTTGTTCATCTCACCCCCAA
* *
8181433 ATTTGTCAACGAAACAAGGCTCATTTGTCATTTCCAAGCGAATTATGCAAGAGATTGGTAGTTGT
66 ATTTGTCAAAGAAACAAGGCTAATTTGTCATTTCCAAGCGAATTATGCAAGAGATTGGTAGTTGT
8181498 TGTGTCATTTTCTTTCTACATTAAAAAAAAAAGACAAAAAAAGAAAAAAAAAACGAAGATTAAGT
131 TGTGTCATTTTCTTTCTACATT-AAAAAAAAAGACAAAAAAAGAAAAAAAAAACGAAGATTAAGT
8181563 GTCCTGTCTGTGAATATAGTGCAAGA
195 GTCCTGTCTGTGAATATAGTGCAAGA
* *
8181589 CGATTCACGCGTTAAGAAAATTGATTTTACCTCTACCAATGTGTTTTTGTTCATCTCACCCCCAA
1 CGATTCACGCGTTAAGAAAATTGACTTTACCCCTACCAATGTGTTTTTGTTCATCTCACCCCCAA
8181654 ATTTGTCAAAGAAACAAGGCTAATTTGTCATTTCCAAGCGAATTATGCAAGAGATTGGTAGTTGT
66 ATTTGTCAAAGAAACAAGGCTAATTTGTCATTTCCAAGCGAATTATGCAAGAGATTGGTAGTTGT
8181719 TGTGTCATTTTCTTTCTACATT-AAAAAAAAGACAAAAAAAGAAAAAAAAAACGAAGATTAAGTG
131 TGTGTCATTTTCTTTCTACATTAAAAAAAAAGACAAAAAAAGAAAAAAAAAACGAAGATTAAGTG
8181783 TCCTGTCTGTGAATATAGTGCAAGA
196 TCCTGTCTGTGAATATAGTGCAAGA
8181808 GCCCCCACAT
Statistics
Matches: 215, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
219 67 0.31
221 148 0.69
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (220 bp):
CGATTCACGCGTTAAGAAAATTGACTTTACCCCTACCAATGTGTTTTTGTTCATCTCACCCCCAA
ATTTGTCAAAGAAACAAGGCTAATTTGTCATTTCCAAGCGAATTATGCAAGAGATTGGTAGTTGT
TGTGTCATTTTCTTTCTACATTAAAAAAAAAGACAAAAAAAGAAAAAAAAAACGAAGATTAAGTG
TCCTGTCTGTGAATATAGTGCAAGA
Found at i:8196952 original size:26 final size:26
Alignment explanation
Indices: 8196916--8196966 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
8196906 GGGAATTATT
*
8196916 GGTTTGATTTGTATATGCACACTATC
1 GGTTTGATTTGTATATACACACTATC
*
8196942 GGTTTGGTTTGTATATACACACTAT
1 GGTTTGATTTGTATATACACACTAT
8196967 TTTCATACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (26 bp):
GGTTTGATTTGTATATACACACTATC
Found at i:8201572 original size:2 final size:2
Alignment explanation
Indices: 8201565--8201600 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8201555 AAGAAATTGT
8201565 TA TA TA TA 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 TA TA TA TA
8201601 ATCTTGCGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8206599 original size:27 final size:29
Alignment explanation
Indices: 8206530--8206603 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
8206520 AAGTATGGTA
8206530 TAGGGA-TGAAATTGAATAAAGATTCATTG
1 TAGGGACT-AAATTGAATAAAGATTCATTG
*
8206559 TAGGAGAACTAAATTGAATAAA-ATTTATT-
1 TAGG-G-ACTAAATTGAATAAAGATTCATTG
8206588 TAGGGACTAAATTGAA
1 TAGGGACTAAATTGAA
8206604 CTCAAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 11 0.27
28 1 0.02
29 8 0.20
30 7 0.17
31 13 0.32
32 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (29 bp):
TAGGGACTAAATTGAATAAAGATTCATTG
Found at i:8207104 original size:19 final size:19
Alignment explanation
Indices: 8207076--8207115 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
8207066 AGCATGGCAG
8207076 CATGGGAGCAACATTTACA
1 CATGGGAGCAACATTTACA
*
8207095 CATGGTAGCAACATTTACA
1 CATGGGAGCAACATTTACA
8207114 CA
1 CA
8207116 AAATTAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (19 bp):
CATGGGAGCAACATTTACA
Found at i:8207956 original size:24 final size:24
Alignment explanation
Indices: 8207897--8207950 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
8207887 GATCCAACAA
8207897 TAGCTTCACTTGGTGCACCACCAG
1 TAGCTTCACTTGGTGCACCACCAG
*
8207921 CAGCTTCACTTGGTGCACCACCAG
1 TAGCTTCACTTGGTGCACCACCAG
8207945 TAGCTT
1 TAGCTT
8207951 TCCTTGCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.26
Consensus pattern (24 bp):
TAGCTTCACTTGGTGCACCACCAG
Found at i:8217203 original size:40 final size:39
Alignment explanation
Indices: 8217055--8217254 Score: 202
Period size: 40 Copynumber: 5.0 Consensus size: 39
8217045 TGTTTAACTA
8217055 GTTGTTTGGATATTTATTTTAGTTATTTAAGTTTATGTT
1 GTTGTTTGGATATTTATTTTAGTTATTTAAGTTTATGTT
* * * * *
8217094 GTTGTTTGGATATATGTGTTTGGTTATCTAGGTTTATGTT
1 GTTGTTTGGATATTTAT-TTTAGTTATTTAAGTTTATGTT
* * * *
8217134 ATTTGTTTGCATCTTTGAGTTTAGTTATTTAAGTTTATGTT
1 -GTTGTTTGGATATTT-ATTTTAGTTATTTAAGTTTATGTT
* * * *
8217175 GTTATTTGAATATTTATATATAGTTATTTAAGTTTATATT
1 GTTGTTTGGATATTTAT-TTTAGTTATTTAAGTTTATGTT
* * * *
8217215 GCTGTATGGATATTTTTTTTTAATTATTTAAGTTTATGTT
1 GTTGTTTGGATA-TTTATTTTAGTTATTTAAGTTTATGTT
8217255 TAAGATCTTA
Statistics
Matches: 127, Mismatches: 29, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
39 16 0.13
40 77 0.61
41 34 0.27
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.58
Consensus pattern (39 bp):
GTTGTTTGGATATTTATTTTAGTTATTTAAGTTTATGTT
Found at i:8221555 original size:21 final size:20
Alignment explanation
Indices: 8221531--8221575 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
8221521 TTAATATAAT
8221531 TTAAAATAAAATAACATAAAA
1 TTAAAATAAAATAAC-TAAAA
* * *
8221552 TTAAACTCAAATAACTTAAA
1 TTAAAATAAAATAACTAAAA
8221572 TTAA
1 TTAA
8221576 CTATTCAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAAATAAAATAACTAAAA
Found at i:8227177 original size:21 final size:22
Alignment explanation
Indices: 8227148--8227196 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
8227138 AAATGATTAA
*
8227148 TTTAAGTTATTTTA-ATTAAAT
1 TTTATGTTATTTTATATTAAAT
*
8227169 TTTATGTTATTTTATTTTAAAT
1 TTTATGTTATTTTATATTAAAT
8227191 TATTAT
1 T-TTAT
8227197 TATTAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 7 0.29
23 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTATGTTATTTTATATTAAAT
Found at i:8227199 original size:21 final size:20
Alignment explanation
Indices: 8227146--8227200 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
8227136 TTAAATGATT
*
8227146 AATTTAAGTTATTTTAATTA
1 AATTTTAGTTATTTTAATTA
*
8227166 AATTTTATGTTATTTTATTTTA
1 AATTTTA-GTTATTTTA-ATTA
8227188 AATTATTA-TTATT
1 AATT-TTAGTTATT
8227201 AATTTCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.20
21 14 0.47
22 7 0.23
23 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
AATTTTAGTTATTTTAATTA
Found at i:8246227 original size:2 final size:2
Alignment explanation
Indices: 8246222--8246258 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8246212 GCTTGATTTA
8246222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8246259 AAGTAATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8246426 original size:23 final size:22
Alignment explanation
Indices: 8246384--8246427 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
8246374 AAAATTCAAA
8246384 AATTAATATTATAAGTAAAAAAT
1 AATTAATATTATAAG-AAAAAAT
8246407 AATTAATTATATATAA-AAAAA
1 AATTAA-TAT-TATAAGAAAAA
8246428 TTATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AATTAATATTATAAGAAAAAAT
Found at i:8246478 original size:14 final size:13
Alignment explanation
Indices: 8246445--8246488 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
8246435 AAATTATTAA
8246445 ATATATATTTTATT
1 ATATAT-TTTTATT
*
8246459 AAATATTTTTATTT
1 ATATATTTTTA-TT
*
8246473 ATATATTTTTAAT
1 ATATATTTTTATT
8246486 ATA
1 ATA
8246489 ATTAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATATTTTTATT
Found at i:8275102 original size:3 final size:3
Alignment explanation
Indices: 8275096--8275134 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
8275086 GAGGTAGGTA
* *
8275096 TGG TGG TGG TGG TGG TGG TGG TAG TGG TGG CGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
8275135 AGCGTAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.03, G:0.64, T:0.31
Consensus pattern (3 bp):
TGG
Found at i:8285660 original size:39 final size:39
Alignment explanation
Indices: 8285603--8285677 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
8285593 TTAGTCAACC
8285603 TGAAACCCTCAAGCGGGTCTTCGAATTCAATTGGAATAA
1 TGAAACCCTCAAGCGGGTCTTCGAATTCAATTGGAATAA
* * *
8285642 TGAAATCCTCAGGTGGGTCTTCGAATTCAATTGGAA
1 TGAAACCCTCAAGCGGGTCTTCGAATTCAATTGGAA
8285678 ATTAGTTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (39 bp):
TGAAACCCTCAAGCGGGTCTTCGAATTCAATTGGAATAA
Found at i:8286523 original size:12 final size:12
Alignment explanation
Indices: 8286506--8286533 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
8286496 GACAAGGGAA
8286506 GAAAGGGTGAGG
1 GAAAGGGTGAGG
8286518 GAAAGGGTGAGG
1 GAAAGGGTGAGG
8286530 GAAA
1 GAAA
8286534 AGATAATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.54, T:0.07
Consensus pattern (12 bp):
GAAAGGGTGAGG
Found at i:8286693 original size:69 final size:69
Alignment explanation
Indices: 8286596--8286748 Score: 292
Period size: 69 Copynumber: 2.2 Consensus size: 69
8286586 TCAGAGAGAC
8286596 AGAGA-GA-GAAGAAGAAGAAGAAGAAGAGAAGGAAGAAAGGGTTGGTCCTTTGTTTTCCTTTAA
1 AGAGAGGAGGAAGAAGAAGAAGAAGAAGAGAAGGAAGAAAGGGTTGGTCCTTTGTTTTCCTTTAA
8286659 AGGG
66 AGGG
8286663 AGAGAGGAGGAAGAAGAAGAAGAAGAAGAGAAGGAAGAAAGGGTTGGTCCTTTGTTTTCCTTTAA
1 AGAGAGGAGGAAGAAGAAGAAGAAGAAGAGAAGGAAGAAAGGGTTGGTCCTTTGTTTTCCTTTAA
8286728 AGGG
66 AGGG
8286732 AGAGAGGAGGAAGAAGA
1 AGAGAGGAGGAAGAAGA
8286749 GAAAGAGAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
67 5 0.06
68 2 0.02
69 77 0.92
ACGTcount: A:0.41, C:0.05, G:0.37, T:0.17
Consensus pattern (69 bp):
AGAGAGGAGGAAGAAGAAGAAGAAGAAGAGAAGGAAGAAAGGGTTGGTCCTTTGTTTTCCTTTAA
AGGG
Found at i:8286902 original size:31 final size:31
Alignment explanation
Indices: 8286842--8286904 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
8286832 TAAGAATGTA
*
8286842 ATTTTTTATAAAAATAATATTATAGTTTTTT
1 ATTTTTTATAAAAATAATATGATAGTTTTTT
8286873 ATTTTTTATAAATCAATAAT-TGATA-TTTTTT
1 ATTTTTTATAAA--AATAATATGATAGTTTTTT
8286904 A
1 A
8286905 AAATTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 19 0.66
32 4 0.14
33 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (31 bp):
ATTTTTTATAAAAATAATATGATAGTTTTTT
Found at i:8288136 original size:118 final size:118
Alignment explanation
Indices: 8287915--8288209 Score: 333
Period size: 118 Copynumber: 2.5 Consensus size: 118
8287905 ATGGTAAAAG
* * * * * *
8287915 AAAACTTGAAATCAATTTTTTAAAATTAAGATATAGAACACGATAATTTTAATTCAAATTCATTT
1 AAAACTTAAAATTAAATTTTCAAAATTAAGATATAAAACACGATAA-TTTAATTCAAATTCACTT
* * * ** *
8287980 AACTGTCAAGTCTGTCATTATTTCTTGTAATGGTAAAAGAAAATTACAGA-TTT
65 AACTGTCAAATCCGTCATTATTTCCTACAATGATAAAAGAAAATTACAGACTTT
* * * * *
8288033 AAATCTTCAAA-TAAATTTCTCAAAATTAAGATACAAAATACGATAATTTAAATCAATATTCACT
1 AAAACTTAAAATTAAATTT-TCAAAATTAAGATATAAAACACGATAATTTAATTCAA-ATTCACT
* * *
8288097 TAATTGTCAAATCCGTTATTATTTCCTACAATGATAAAAGAGAATTACAGACTTT
64 TAACTGTCAAATCCGTCATTATTTCCTACAATGATAAAAGAAAATTACAGACTTT
* * *
8288152 AAAACTTAAAATTAACTTTTTAAAATTAAGATATGAAACACGATAATCTTAATTCAAA
1 AAAACTTAAAATTAAATTTTCAAAATTAAGATATAAAACACGATAAT-TTAATTCAAA
8288210 ATGCAGGATT
Statistics
Matches: 145, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
117 14 0.10
118 80 0.55
119 37 0.26
120 14 0.10
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (118 bp):
AAAACTTAAAATTAAATTTTCAAAATTAAGATATAAAACACGATAATTTAATTCAAATTCACTTA
ACTGTCAAATCCGTCATTATTTCCTACAATGATAAAAGAAAATTACAGACTTT
Found at i:8304433 original size:15 final size:15
Alignment explanation
Indices: 8304399--8304447 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
8304389 AGGATGAGTC
8304399 TGAAGAAGAAGAAAA
1 TGAAGAAGAAGAAAA
* * *
8304414 GGAAGAGGAAGAGAA
1 TGAAGAAGAAGAAAA
*
8304429 TGAAGAAGAGGAAAA
1 TGAAGAAGAAGAAAA
8304444 TGAA
1 TGAA
8304448 AATGGCATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (15 bp):
TGAAGAAGAAGAAAA
Found at i:8315197 original size:20 final size:18
Alignment explanation
Indices: 8315172--8315209 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
8315162 TTTTTTATGA
8315172 TTAAATTTTAATTTAATAAT
1 TTAAATTTT-A-TTAATAAT
8315192 TTAAATTTTATTAATAAT
1 TTAAATTTTATTAATAAT
8315210 ATATATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATTTTATTAATAAT
Found at i:8315542 original size:19 final size:18
Alignment explanation
Indices: 8315514--8315552 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
8315504 CCTCATTATG
8315514 ATTTAATTTTAATTTAATA
1 ATTTAATTTTAA-TTAATA
* *
8315533 ATTTATTTTTTATTAATA
1 ATTTAATTTTAATTAATA
8315551 AT
1 AT
8315553 ATATAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAATTTTAATTAATA
Found at i:8316902 original size:45 final size:45
Alignment explanation
Indices: 8316848--8316946 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 45
8316838 CCCCATCGGC
* *
8316848 TCAATCCCCGGATGCGACTCCGCCTGCTTCTTCGACCGCCCCGGT
1 TCAATCCCCGGATGCGACTCCGCCTGCTTCTTCGACAGCCCCAGT
*
8316893 TCAATCCCCGGCTGCGACTCCGCCTGCTTCTTCGACAGCCCCAGT
1 TCAATCCCCGGATGCGACTCCGCCTGCTTCTTCGACAGCCCCAGT
8316938 TCAATCCCC
1 TCAATCCCC
8316947 AGCGAGTTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.13, C:0.45, G:0.19, T:0.22
Consensus pattern (45 bp):
TCAATCCCCGGATGCGACTCCGCCTGCTTCTTCGACAGCCCCAGT
Found at i:8318260 original size:23 final size:24
Alignment explanation
Indices: 8318225--8318282 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
8318215 ATTTTGAAAA
* *
8318225 ATTTAAATAAAATTTTTTTATTAT
1 ATTTAAATAAAATTCTTATATTAT
*
8318249 ATTT-AATTAAATTCTTATATTATT
1 ATTTAAATAAAATTCTTATATTA-T
8318273 ATCTTAAATA
1 AT-TTAAATA
8318283 TAATAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 15 0.56
24 7 0.26
25 2 0.07
26 3 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAAATAAAATTCTTATATTAT
Found at i:8319085 original size:13 final size:13
Alignment explanation
Indices: 8319062--8319094 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
8319052 AGAATTGATG
8319062 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
8319075 A-AAAAACAGAAAA
1 AGAAAAA-AGAAAA
8319088 AGAAAAA
1 AGAAAAA
8319095 TGGCGTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 8 0.44
14 5 0.28
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:8331045 original size:21 final size:20
Alignment explanation
Indices: 8331008--8331060 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
8330998 TTTTTTTTTA
*
8331008 ATTTTAAATTTTGAGAATAT
1 ATTTTAAATTTTAAGAATAT
* *
8331028 ATTTTAATTTTTTAAGAATTTT
1 ATTTTAA-ATTTTAAGAA-TAT
8331050 ATTTTTAAATT
1 A-TTTTAAATT
8331061 ATCAAATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 5 0.19
23 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTAAATTTTAAGAATAT
Found at i:8331722 original size:17 final size:17
Alignment explanation
Indices: 8331700--8331749 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
8331690 TTATTTAAAC
8331700 TTTTTTTAAAAATTTTA
1 TTTTTTTAAAAATTTTA
** *
8331717 -TTTTTTAAAAATACTC
1 TTTTTTTAAAAATTTTA
8331733 TTTTTTTAAATAATTTT
1 TTTTTTTAAA-AATTTT
8331750 TTTAAAATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 13 0.50
17 9 0.35
18 4 0.15
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTTAAAAATTTTA
Found at i:8331736 original size:16 final size:15
Alignment explanation
Indices: 8331700--8331756 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
8331690 TTATTTAAAC
**
8331700 TTTTTTTAAAAATTT
1 TTTTTTTAAAAATAA
*
8331715 TATTTTTTAAAAATAC
1 T-TTTTTTAAAAATAA
*
8331731 TCTTTTTT-TAAATAA
1 T-TTTTTTAAAAATAA
8331746 TTTTTTTAAAA
1 TTTTTTTAAAA
8331757 TCTTATTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 6 0.18
15 9 0.26
16 19 0.56
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTTAAAAATAA
Found at i:8345698 original size:16 final size:16
Alignment explanation
Indices: 8345677--8345707 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8345667 AATAATTGAC
8345677 TAAGGATGTTGATATT
1 TAAGGATGTTGATATT
8345693 TAAGGATGTTGATAT
1 TAAGGATGTTGATAT
8345708 GTTGCTAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
TAAGGATGTTGATATT
Found at i:8352599 original size:38 final size:38
Alignment explanation
Indices: 8352551--8352626 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
8352541 GGATATTTCT
*
8352551 TGAGTCTGTTGCCTAATATTTCTCAAATGTTATCTGAC
1 TGAGTCTGTTGCCTAATATTTCTCAAATCTTATCTGAC
* ** * *
8352589 TGAGTTTGTTGCCTGTTATTTCTTAAATCTTATTTGAC
1 TGAGTCTGTTGCCTAATATTTCTCAAATCTTATCTGAC
8352627 CCAGATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (38 bp):
TGAGTCTGTTGCCTAATATTTCTCAAATCTTATCTGAC
Found at i:8352735 original size:98 final size:98
Alignment explanation
Indices: 8352566--8352750 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 98
8352556 CTGTTGCCTA
* * *
8352566 ATATTTCTCAAATGTTATCTGACTGAGTTTGTTGCCTGTTATTTCTTAAATCTTATTTGACCCAG
1 ATATTTCTCAAATGTTATCTGACTGAGTTTGTTGCCTGATATTTCTTAAATCTTATCTGACCCAA
8352631 ATATTTGTTAAATGTTATTTGATATATTGCTTG
66 ATATTTGTTAAATGTTATTTGATATATTGCTTG
* * ** *
8352664 ATATTTCTCAAACT-TTCTTTGACTGAGTTTGTTGTTTGATATTTCTTAAA-CTTTATCTGACTC
1 ATATTTCTCAAA-TGTTATCTGACTGAGTTTGTTGCCTGATATTTCTTAAATC-TTATCTGACCC
8352727 AAATATTTGTTAAATGTTATTTGA
64 AAATATTTGTTAAATGTTATTTGA
8352751 CTTAATTTCC
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 1 0.01
98 75 0.97
99 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (98 bp):
ATATTTCTCAAATGTTATCTGACTGAGTTTGTTGCCTGATATTTCTTAAATCTTATCTGACCCAA
ATATTTGTTAAATGTTATTTGATATATTGCTTG
Found at i:8353256 original size:107 final size:107
Alignment explanation
Indices: 8353043--8353257 Score: 290
Period size: 107 Copynumber: 2.0 Consensus size: 107
8353033 AAAAAGAAGA
* * *
8353043 ACAAAAATTAGTAAAGATAATTAAATAATGAAAAACATCTACTCTTTGGCTTGACAACAGATAAT
1 ACAAAAATTAGTAAAGATAATTAAACAATGAAAAACATCTACTCTTTGGATTGACAACAAATAAT
* **
8353108 AAAAATCAACGTACTCGGAGTGGTATGGATACGCAGCTGAGG
66 AAAAATCAACGTACTCGGAGTGGTATAGATACGCAAATGAGG
8353150 ACAAAAATTAGTAAAGATAATTAAACAATGAAAAACA-CTTACTCTTTGGATTGACAACAAATAA
1 ACAAAAATTAGTAAAGATAATTAAACAATGAAAAACATC-TACTCTTTGGATTGACAACAAATAA
* ** * * *
8353214 TAGAAATCAGTGTACTC-GAGGTGGTCTAGCTATGCAAATGAGG
65 TAAAAATCAACGTACTCGGA-GTGGTATAGATACGCAAATGAGG
8353257 A
1 A
8353258 AGAATTAAGG
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 3 0.03
107 91 0.97
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (107 bp):
ACAAAAATTAGTAAAGATAATTAAACAATGAAAAACATCTACTCTTTGGATTGACAACAAATAAT
AAAAATCAACGTACTCGGAGTGGTATAGATACGCAAATGAGG
Found at i:8354218 original size:116 final size:118
Alignment explanation
Indices: 8354008--8354243 Score: 388
Period size: 116 Copynumber: 2.0 Consensus size: 118
8353998 ATTGATAGTA
*
8354008 TATACTTCTTTCACTTTTTTTTTTTATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAG
1 TATACTTCTTTCAC-TTTTTTTTTTATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAA
*
8354073 GAGAATTATGCATCAACAATGACCTAAATGCTTGAGTGCATAATTTTCTTTAAC
65 GAGAATTATGCATCAACAATAACCTAAATGCTTGAGTGCATAATTTTCTTTAAC
*
8354127 TATACTTCTTTCAC-TTTTTTTTTATAATTGGAGA-GGGGGATTCAAACCTGCTGTTTAGGCAAG
1 TATACTTCTTTCACTTTTTTTTTTATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAAG
* *
8354190 AGGATTATGCATCAACAATAAGCC-AAATGCTTGAGTGCATATTTTTCTTTAAC
66 AGAATTATGCATCAACAATAA-CCTAAATGCTTGAGTGCATAATTTTCTTTAAC
8354243 T
1 T
8354244 TCAATTAATT
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
116 75 0.68
117 22 0.20
119 14 0.13
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (118 bp):
TATACTTCTTTCACTTTTTTTTTTATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAAG
AGAATTATGCATCAACAATAACCTAAATGCTTGAGTGCATAATTTTCTTTAAC
Found at i:8354270 original size:116 final size:117
Alignment explanation
Indices: 8354033--8354271 Score: 272
Period size: 116 Copynumber: 2.1 Consensus size: 117
8354023 TTTTTTTTTT
* *
8354033 ATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAGGAGAATTATGCATCAACAATGACCT
1 ATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAAGAGAATTATGCATCAACAATAACCT
* * *** *****
8354098 AAATGCTTGAGTGCATAATTTTCTTTAACTATACTTCTTTCACTTTTTTTTT
66 AAATGCTTGAGTGCATAATTTTCTTTAACTATAATTATTTCACAGATAAAAA
* *
8354150 ATAATTGGAGA-GGGGGATTCAAACCTGCTGTTTAGGCAAGAGGATTATGCATCAACAATAAGCC
1 ATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAAGAGAATTATGCATCAACAATAA-CC
*
8354214 -AAATGCTTGAGTGCATATTTTTCTTTAACT-TCAATTAATTAT-A-AGATAAAAA
65 TAAATGCTTGAGTGCATAATTTTCTTTAACTAT-AATT-ATT-TCACAGATAAAAA
8354266 ATAATT
1 ATAATT
8354272 CTAATAAGGA
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
115 1 0.01
116 85 0.83
117 16 0.16
118 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (117 bp):
ATAATTGGAGAGGGGGGATTCAAACCTGCTATTTAGGCAAGAGAATTATGCATCAACAATAACCT
AAATGCTTGAGTGCATAATTTTCTTTAACTATAATTATTTCACAGATAAAAA
Found at i:8357807 original size:2 final size:2
Alignment explanation
Indices: 8357800--8357837 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
8357790 AACTGTTTTT
* *
8357800 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8357838 TGAGTTTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8364966 original size:24 final size:23
Alignment explanation
Indices: 8364934--8365015 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
8364924 GATATATTGA
8364934 TGTCACGGTCTTACAAGAGAGCTG
1 TGTCACGGTCTTACAAGAGAG-TG
** *
8364958 TGTCACGGTCTTA-TTGGGTAGTCG
1 TGTCACGGTCTTACAAGAG-AGT-G
**
8364982 TGTCACGGTCACACAAGAGAGGTG
1 TGTCACGGTCTTACAAGAGA-GTG
8365006 TGTCACGGTC
1 TGTCACGGTC
8365016 ATATTGGGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
23 3 0.07
24 39 0.85
25 4 0.09
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (23 bp):
TGTCACGGTCTTACAAGAGAGTG
Found at i:8365008 original size:48 final size:48
Alignment explanation
Indices: 8364934--8365029 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
8364924 GATATATTGA
** *
8364934 TGTCACGGTCTTACAAGAGAGCTGTGTCACGGTCTTATTGGGTAGTCG
1 TGTCACGGTCACACAAGAGAGCTGTGTCACGGTCATATTGGGTAGTCG
*
8364982 TGTCACGGTCACACAAGAGAGGTGTGTCACGGTCATATTGGGTAGTCG
1 TGTCACGGTCACACAAGAGAGCTGTGTCACGGTCATATTGGGTAGTCG
8365030 ATTGAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (48 bp):
TGTCACGGTCACACAAGAGAGCTGTGTCACGGTCATATTGGGTAGTCG
Found at i:8365512 original size:47 final size:48
Alignment explanation
Indices: 8365415--8365513 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 48
8365405 TAAGTTATTT
* ***
8365415 TTCATCAATTATGAATTGACATATATATTTTTTTCTATATTGTAATTA
1 TTCATCAATTATGAATTGACATATATATTTTTTTCGATACCATAATTA
** * *
8365463 TTCATCAATTATGGGTTGATATATGTA-TTTTTTCGATACCATAATTA
1 TTCATCAATTATGAATTGACATATATATTTTTTTCGATACCATAATTA
8365510 TTCA
1 TTCA
8365514 CCGGAGATGT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 20 0.47
48 23 0.53
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.49
Consensus pattern (48 bp):
TTCATCAATTATGAATTGACATATATATTTTTTTCGATACCATAATTA
Found at i:8367204 original size:21 final size:19
Alignment explanation
Indices: 8367153--8367204 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
8367143 AAATTGAGTC
8367153 ATTTTATTTTAT-TTTAATT
1 ATTTTATTTT-TGTTTAATT
8367172 ATTTT-TTCTTTGCTTTAAATT
1 ATTTTATT-TTTG-TTT-AATT
8367193 ATTTTATTTTTG
1 ATTTTATTTTTG
8367205 GGATAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 3 0.11
19 7 0.25
20 3 0.11
21 13 0.46
22 2 0.07
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTATTTTTGTTTAATT
Found at i:8367221 original size:118 final size:119
Alignment explanation
Indices: 8367018--8367240 Score: 292
Period size: 118 Copynumber: 1.9 Consensus size: 119
8367008 TAAAAATTGA
* *
8367018 AAAAAAATTGAGTCCTTTTTTTCTTTTATTTTAATAATTTTTTATTTGCTTTAAAGTATTTATTT
1 AAAAAAATTGAGTCC-TATTTTATTTTATTTTAATAATTTTTTATTTGCTTTAAAGTATTTATTT
* * **
8367083 TTGTGATTAAAGAAGGAAAAAAAGGAAAAATTTCAAAACCTGGAGATTAAAAAAAG
65 TTGGGATAAAAGAA-GAAAAAAAGGAAAAATGGCAAAACCTGGAGATTAAAAAAAG
* * *
8367139 AAAAAAATTGAGT-C-ATTTTATTTTATTTTAATTATTTTTTCTTTGCTTTAAATTATTTTATTT
1 AAAAAAATTGAGTCCTATTTTATTTTATTTTAATAATTTTTTATTTGCTTTAAAGTA-TTTATTT
8367202 TTGGGATAAAAG--GAAAAAAAGGGGAAAAATGGCAAAACC
65 TTGGGATAAAAGAAGAAAAAAA--GGAAAAATGGCAAAACC
8367241 GGGGAAAAGG
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
116 8 0.09
118 51 0.57
119 17 0.19
120 1 0.01
121 13 0.14
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (119 bp):
AAAAAAATTGAGTCCTATTTTATTTTATTTTAATAATTTTTTATTTGCTTTAAAGTATTTATTTT
TGGGATAAAAGAAGAAAAAAAGGAAAAATGGCAAAACCTGGAGATTAAAAAAAG
Found at i:8369054 original size:106 final size:106
Alignment explanation
Indices: 8368866--8369181 Score: 483
Period size: 106 Copynumber: 3.0 Consensus size: 106
8368856 AAGATGCCTC
* *
8368866 TTAACTTGTAAAACTGAACCTTTA-TCCTGGATT-AAGTTTACAGGAATGGTGATAGAGTAGGTT
1 TTAACTTGTAAAACTGAACCTTTACT-CTGG-TTGAAGTTAACAGGAATGGTGATAGAGTAAGTT
*
8368929 CAATCCATGGTTCACAGATTGGTAAGAAAGTAGAATTGCTCTG
64 CAATCCATGGCTCACAGATTGGTAAGAAAGTAGAATTGCTCTG
* * *
8368972 TTAACTTGCAAAACTGAACCTTTACTCTGGTTGAAGTTAACAGGAATGGTGATAGAGAAAGTGCA
1 TTAACTTGTAAAACTGAACCTTTACTCTGGTTGAAGTTAACAGGAATGGTGATAGAGTAAGTTCA
* * *
8369037 ATCCATGGCTCATAGATTGGTGAGAAAGTAGAATTGCCCTG
66 ATCCATGGCTCACAGATTGGTAAGAAAGTAGAATTGCTCTG
* * *
8369078 TTAACTTGTAAAACTGAACCTTTACCCTGGCTGAGGTTAACAGGAATGGTGATAGAGTTAAGTTC
1 TTAACTTGTAAAACTGAACCTTTACTCTGGTTGAAGTTAACAGGAATGGTGATAGAG-TAAGTTC
8369143 AATCCATGGCTCACAGATTGGTAAGAAAGTAGAATTGCT
65 AATCCATGGCTCACAGATTGGTAAGAAAGTAGAATTGCT
8369182 GCTGCTATCC
Statistics
Matches: 189, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
105 2 0.01
106 145 0.77
107 42 0.22
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (106 bp):
TTAACTTGTAAAACTGAACCTTTACTCTGGTTGAAGTTAACAGGAATGGTGATAGAGTAAGTTCA
ATCCATGGCTCACAGATTGGTAAGAAAGTAGAATTGCTCTG
Found at i:8369287 original size:32 final size:32
Alignment explanation
Indices: 8369246--8369310 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
8369236 TTATTTAATC
*
8369246 AATTATGGTCTTTTACAGAAAAGAGTTAAAAG
1 AATTATGGTCTTTTACAGAAAAGAATTAAAAG
* *
8369278 AATTATGGTCTTTTACAGATAAGAATTTAAAG
1 AATTATGGTCTTTTACAGAAAAGAATTAAAAG
8369310 A
1 A
8369311 TTTGTTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (32 bp):
AATTATGGTCTTTTACAGAAAAGAATTAAAAG
Found at i:8379580 original size:8 final size:8
Alignment explanation
Indices: 8379567--8379596 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
8379557 GCTGAAGATT
8379567 AAAAAAAC
1 AAAAAAAC
8379575 AAAAAAAC
1 AAAAAAAC
8379583 AAAAAAAC
1 AAAAAAAC
8379591 AAAAAA
1 AAAAAA
8379597 TTGTAGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:8380201 original size:2 final size:2
Alignment explanation
Indices: 8380194--8380222 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8380184 CTTATTTCTT
8380194 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 T
8380223 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8392250 original size:102 final size:102
Alignment explanation
Indices: 8392073--8392271 Score: 337
Period size: 102 Copynumber: 2.0 Consensus size: 102
8392063 TTAATAAGAG
8392073 ACATCATTCAAAGATTCAATTTTGCAGATTAAAGGGGAACAAAGCAATGATCCTACACCCTTTCC
1 ACATCATTCAAAGATTCAATTTTGCAGATTAAAGGGGAACAAAGCAATGATCCTACACCCTTTCC
*
8392138 TCATAGCAATTAC-GATGAATTTACACCAAAGTTAGAT
66 TCATAACAATTACAG-TGAATTTACACCAAAGTTAGAT
** * *
8392175 ACATCATTCAAAGATTCAATTTTGCAGATTAAAGGGGAATGAAGCAATGATCCTACTCGCTTTCC
1 ACATCATTCAAAGATTCAATTTTGCAGATTAAAGGGGAACAAAGCAATGATCCTACACCCTTTCC
8392240 TCATAACAATTACAGTGAATTTACACCAAAGT
66 TCATAACAATTACAGTGAATTTACACCAAAGT
8392272 CCTATATTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 90 0.99
103 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (102 bp):
ACATCATTCAAAGATTCAATTTTGCAGATTAAAGGGGAACAAAGCAATGATCCTACACCCTTTCC
TCATAACAATTACAGTGAATTTACACCAAAGTTAGAT
Found at i:8392970 original size:3 final size:3
Alignment explanation
Indices: 8392962--8392986 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8392952 TATGGCAGAA
8392962 GCG GCG GCG GCG GCG GCG GCG GCG G
1 GCG GCG GCG GCG GCG GCG GCG GCG G
8392987 TGAGGGCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GCG
Found at i:8393468 original size:2 final size:2
Alignment explanation
Indices: 8393461--8393486 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8393451 GCATTCATTA
8393461 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
8393487 TCAATATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8404902 original size:193 final size:189
Alignment explanation
Indices: 8404605--8404957 Score: 537
Period size: 193 Copynumber: 1.8 Consensus size: 189
8404595 TGATAAAAAG
* *
8404605 AACAGAAATGGCCAAATGGGTTGGAATCTTACACACTGTTTGACATGCAGGTCAGTCCATGACCT
1 AACAGAAATGGCCAAATGGGTGGGAATCTTACACACTGTTTGACATGCAGGCCAGTCCATGACCT
* * * *
8404670 GTAAAAGTATGAAATAACCAGTAATCCAACCACCCATTTTGCACTCATGGTGGCAGCTCAAAGCA
66 GTAAAAGAATGAAATAACCAGTAACCCAACCACCCATTTTGCACT-A---TAGCACCT-AAAGCA
*
8404735 ATCGGGCTGGGGTT-AGACTTCAACTTTTGCATCCCCTAAACCGATCTGTCCCCTTATAAAGCC
126 ATCGGGCTGGGGTTAAGACTTCAACTTATGCATCCCCTAAACCGATCTGTCCCCTTATAAAGCC
*
8404798 AACAGAAATGGCCAAATGGGTGGGAATCTTACACATTGTTTGACATGCAGGCCAGTCCATGACCT
1 AACAGAAATGGCCAAATGGGTGGGAATCTTACACACTGTTTGACATGCAGGCCAGTCCATGACCT
* * *
8404863 GTAAAAGAATGAAATAGCCAGTAACCCAACCATCCATTTTGCACTATAGCACCTAAATCAATCGG
66 GTAAAAGAATGAAATAACCAGTAACCCAACCACCCATTTTGCACTATAGCACCTAAAGCAATCGG
* *
8404928 GCTGGTGTTAAGACTTTAACTTATGCATCC
131 GCTGGGGTTAAGACTTCAACTTATGCATCC
8404958 TTTAAACCAA
Statistics
Matches: 146, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
188 18 0.12
189 24 0.16
192 1 0.01
193 103 0.71
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (189 bp):
AACAGAAATGGCCAAATGGGTGGGAATCTTACACACTGTTTGACATGCAGGCCAGTCCATGACCT
GTAAAAGAATGAAATAACCAGTAACCCAACCACCCATTTTGCACTATAGCACCTAAAGCAATCGG
GCTGGGGTTAAGACTTCAACTTATGCATCCCCTAAACCGATCTGTCCCCTTATAAAGCC
Found at i:8407505 original size:194 final size:194
Alignment explanation
Indices: 8407176--8407593 Score: 660
Period size: 194 Copynumber: 2.2 Consensus size: 194
8407166 GCACTCATAG
* **
8407176 TCATGGTGGCAGCTCAAAGCAATGGGGCTGGGGTTAGACTTCCAACTTATGCATCCCTTAAACCA
1 TCATGGTGGCAGCTCAAAGCAATGGGGCTGGGGTGAGACTTCCAACTTATGCATCCCCAAAACCA
* *
8407241 ATCTGTTCCCTGATAAAAACAACAGCAATAGCCAAATGGGTTGGAACCTTACACATTGTTTGACA
66 ATCTGTTCCCTGACAAAAACAACAGAAATAGCCAAATGGGTTGGAACCTTACACATTGTTTGACA
* **
8407306 TGCAGGCCAGTCCATGACCCGTAAAAGTATGAAAGAACCAGCAATCCGGCCACCCATTTTGCAC
131 TGCAGGCCAGTCCATGACCCGTAAAAGTATGAAACAACCAGCAATCCAACCACCCATTTTGCAC
*
8407370 TCATGGTGGCAGCTCAAAGCAATGGGGCTGGTGG-GAGACTTCTAACTTATGCATCCCCAAAACC
1 TCATGGTGGCAGCTCAAAGCAATGGGGCTGG-GGTGAGACTTCCAACTTATGCATCCCCAAAACC
* * *
8407434 AATTTGTTTCCTGACAAAAACAACAGAAAT-GTCCAAATGGGTTGGAACCTTACACATTGTTTTA
65 AATCTGTTCCCTGACAAAAACAACAGAAATAG-CCAAATGGGTTGGAACCTTACACATTGTTTGA
* *
8407498 CATGCAGGCCAGTCCATGACCTGTAAACGTATGAAACAACCAGCAATCCAACCACCCATTTTGCA
129 CATGCAGGCCAGTCCATGACCCGTAAAAGTATGAAACAACCAGCAATCCAACCACCCATTTTGCA
8407563 C
194 C
* *
8407564 TCATGGTAGCACCTCAAAGCAATGGGGCTG
1 TCATGGTGGCAGCTCAAAGCAATGGGGCTG
8407594 AGGCTAGACT
Statistics
Matches: 206, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
193 1 0.00
194 203 0.99
195 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (194 bp):
TCATGGTGGCAGCTCAAAGCAATGGGGCTGGGGTGAGACTTCCAACTTATGCATCCCCAAAACCA
ATCTGTTCCCTGACAAAAACAACAGAAATAGCCAAATGGGTTGGAACCTTACACATTGTTTGACA
TGCAGGCCAGTCCATGACCCGTAAAAGTATGAAACAACCAGCAATCCAACCACCCATTTTGCAC
Found at i:8408097 original size:41 final size:41
Alignment explanation
Indices: 8408046--8408133 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
8408036 AAACTAAAAT
* *
8408046 TTTTATGTTATTTCATAGCATAATTAATAACCCAAAGTTCCA
1 TTTT-TGTTATTTCATAGAAAAATTAATAACCCAAAGTTCCA
* *
8408088 TTTTTGTTATTTCATGGAAAAATTTATAACCCAAAGTTCCA
1 TTTTTGTTATTTCATAGAAAAATTAATAACCCAAAGTTCCA
8408129 TTTTT
1 TTTTT
8408134 CTATTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 38 0.90
42 4 0.10
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (41 bp):
TTTTTGTTATTTCATAGAAAAATTAATAACCCAAAGTTCCA
Found at i:8408378 original size:24 final size:25
Alignment explanation
Indices: 8408328--8408379 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
8408318 ATTTTATATT
8408328 AATTTAAATTCATTTTTATATAAAA
1 AATTTAAATTCATTTTTATATAAAA
*
8408353 AATTTAAATTCATTTTTATAAAAAA
1 AATTTAAATTCATTTTTATATAAAA
8408378 AA
1 AA
8408380 ATAAGAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTTAAATTCATTTTTATATAAAA
Found at i:8408388 original size:26 final size:25
Alignment explanation
Indices: 8408333--8408388 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
8408323 ATATTAATTT
* * *
8408333 AAATTCATTTTTATATAAAAAATTT
1 AAATTCATTTTTATAAAAAAAAATA
8408358 AAATTCATTTTTATAAAAAAAAATA
1 AAATTCATTTTTATAAAAAAAAATA
8408383 AGAATT
1 A-AATT
8408389 GGGTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATTCATTTTTATAAAAAAAAATA
Found at i:8409733 original size:17 final size:17
Alignment explanation
Indices: 8409713--8409762 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
8409703 TTCTCCACTT
8409713 CTCTCTCTTTTCTCTTC
1 CTCTCTCTTTTCTCTTC
8409730 CTCT-TCTTTT-TC-T-
1 CTCTCTCTTTTCTCTTC
8409743 CTCTCTCTTTCTCTCTTC
1 CTCTCTCTTT-TCTCTTC
8409761 CT
1 CT
8409763 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 3 0.11
16 8 0.29
17 5 0.18
18 2 0.07
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
CTCTCTCTTTTCTCTTC
Found at i:8409735 original size:30 final size:31
Alignment explanation
Indices: 8409701--8409766 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
8409691 TATTACAATT
8409701 TCTTCTCCACT-TCTCTCTCTTT-TCTCTTCC
1 TCTTCT-CACTCTCTCTCTCTTTCTCTCTTCC
***
8409731 TCTTCTTTTTCTCTCTCTCTTTCTCTCTTCC
1 TCTTCTCACTCTCTCTCTCTTTCTCTCTTCC
8409762 T-TTCT
1 TCTTCT
8409767 TTCTTTGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 21 0.68
31 9 0.29
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (31 bp):
TCTTCTCACTCTCTCTCTCTTTCTCTCTTCC
Found at i:8409764 original size:12 final size:13
Alignment explanation
Indices: 8409714--8409771 Score: 59
Period size: 12 Copynumber: 4.6 Consensus size: 13
8409704 TCTCCACTTC
*
8409714 TCTCTCTTTTCTCT
1 TCTCTCTTCTCT-T
*
8409728 TC-CTCTTCTTTT
1 TCTCTCTTCTCTT
8409740 TCTCTC-TCTCTT
1 TCTCTCTTCTCTT
8409752 TCTCTCTTC-CTT
1 TCTCTCTTCTCTT
*
8409764 TCTTTCTT
1 TCTCTCTT
8409772 TGATCTCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 24 0.63
13 12 0.32
14 2 0.05
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTCTCTTCTCTT
Found at i:8409767 original size:30 final size:30
Alignment explanation
Indices: 8409712--8409768 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
8409702 CTTCTCCACT
8409712 TCTCTCTCTTTTCTCTTCCTCTTCTTTTTC
1 TCTCTCTCTTTTCTCTTCCTCTTCTTTTTC
8409742 TCTCTCTCTTTCTCTCTTCCT-TTCTTT
1 TCTCTCTCTTT-TCTCTTCCTCTTCTTT
8409769 CTTTGATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (30 bp):
TCTCTCTCTTTTCTCTTCCTCTTCTTTTTC
Found at i:8423782 original size:20 final size:20
Alignment explanation
Indices: 8423757--8423794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8423747 CTCTCTTCCT
*
8423757 TTCTTTCCTTCCCTTTTTTG
1 TTCTTTCCTTCCATTTTTTG
*
8423777 TTCTTTTCTTCCATTTTT
1 TTCTTTCCTTCCATTTTT
8423795 CCTTCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.68
Consensus pattern (20 bp):
TTCTTTCCTTCCATTTTTTG
Found at i:8423800 original size:20 final size:20
Alignment explanation
Indices: 8423752--8423801 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
8423742 TTTTCCTCTC
*
8423752 TTCCTTTCTTTCCTTCCCTTT
1 TTCC-TTCTTTCCTTCCATTT
** *
8423773 TTTGTTCTTTTCTTCCATTT
1 TTCCTTCTTTCCTTCCATTT
8423793 TTCCTTCTT
1 TTCCTTCTT
8423802 CTTTCTTGCT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (20 bp):
TTCCTTCTTTCCTTCCATTT
Found at i:8423895 original size:2 final size:2
Alignment explanation
Indices: 8423888--8423912 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8423878 TTTAATTGCT
8423888 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 T
8423913 GAGGGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8430645 original size:23 final size:23
Alignment explanation
Indices: 8430610--8430655 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8430600 GTTTAATGTC
* *
8430610 TTAAAAGTGCAAGAAAAAAAAAT
1 TTAAAAATACAAGAAAAAAAAAT
**
8430633 TTAAAAATACAAGAGTAAAAAAT
1 TTAAAAATACAAGAAAAAAAAAT
8430656 CAGAAACATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.65, C:0.04, G:0.11, T:0.20
Consensus pattern (23 bp):
TTAAAAATACAAGAAAAAAAAAT
Found at i:8430746 original size:12 final size:12
Alignment explanation
Indices: 8430729--8430763 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
8430719 TAAATATGAT
8430729 TTATTTTTATAA
1 TTATTTTTATAA
8430741 TTATTTTTA-AA
1 TTATTTTTATAA
*
8430752 ATATTTTTATAA
1 TTATTTTTATAA
8430764 GAAAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATTTTTATAA
Found at i:8430756 original size:11 final size:12
Alignment explanation
Indices: 8430730--8430763 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
8430720 AAATATGATT
*
8430730 TATTTTTATAAT
1 TATTTTTATAAA
8430742 TATTTTTA-AAA
1 TATTTTTATAAA
8430753 TATTTTTATAA
1 TATTTTTATAA
8430764 GAAAAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTTTATAAA
Found at i:8443023 original size:22 final size:23
Alignment explanation
Indices: 8442998--8443043 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
8442988 TGCTTTATTG
8442998 ATCT-AAA-GCTCAACCATAGCAA
1 ATCTAAAAGGCTCAACCAT-GCAA
8443020 ATCTAAAAGGCTCAACCATGCAA
1 ATCTAAAAGGCTCAACCATGCAA
8443043 A
1 A
8443044 AAGTTTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (23 bp):
ATCTAAAAGGCTCAACCATGCAA
Found at i:8445433 original size:17 final size:18
Alignment explanation
Indices: 8445405--8445438 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8445395 ATTTGATTGC
8445405 ACAAACATCAAAAACTAT
1 ACAAACATCAAAAACTAT
*
8445423 ACAAA-ATCAAATACTA
1 ACAAACATCAAAAACTA
8445439 ACAGACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (18 bp):
ACAAACATCAAAAACTAT
Found at i:8446270 original size:22 final size:20
Alignment explanation
Indices: 8446245--8446288 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
8446235 TAAAAATTTT
*
8446245 AATTTTGATGTATTTAATATTA
1 AATTTTAAT-TATTTAA-ATTA
*
8446267 AATTTTAATTTTTTAAATTA
1 AATTTTAATTATTTAAATTA
8446287 AA
1 AA
8446289 GAATTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTTAATTATTTAAATTA
Found at i:8449871 original size:12 final size:12
Alignment explanation
Indices: 8449854--8449879 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8449844 ATCACTCCCA
8449854 TGCTTAGCTTTG
1 TGCTTAGCTTTG
8449866 TGCTTAGCTTTG
1 TGCTTAGCTTTG
8449878 TG
1 TG
8449880 TATATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.27, T:0.50
Consensus pattern (12 bp):
TGCTTAGCTTTG
Found at i:8458987 original size:2 final size:2
Alignment explanation
Indices: 8458980--8459004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8458970 CTCCACTTGC
8458980 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 T
8459005 TGTATCATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8462620 original size:22 final size:21
Alignment explanation
Indices: 8462582--8462622 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
8462572 TTGTTGTTGG
8462582 GTTTATTTATGTGGATTGCTT
1 GTTTATTTATGTGGATTGCTT
* *
8462603 GTTTAATTTGTGTTGATTGC
1 GTTT-ATTTATGTGGATTGC
8462623 CACAGTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.15, C:0.05, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTATTTATGTGGATTGCTT
Found at i:8477290 original size:2 final size:2
Alignment explanation
Indices: 8477283--8477314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8477273 GTATTGATAC
8477283 TA TA 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 TA TA
8477315 GCAAGCCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8484671 original size:22 final size:22
Alignment explanation
Indices: 8484628--8484672 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8484618 TTGTTATTGG
*
8484628 GTTTTGATTAGGGTTTTGTGTT
1 GTTTTGATTAGGGTTTAGTGTT
*
8484650 GTTTTTATT-GGGTTTAGCTGTT
1 GTTTTGATTAGGGTTTAG-TGTT
8484672 G
1 G
8484673 AAAGGTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.09, C:0.02, G:0.31, T:0.58
Consensus pattern (22 bp):
GTTTTGATTAGGGTTTAGTGTT
Found at i:8493186 original size:46 final size:46
Alignment explanation
Indices: 8493129--8493220 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
8493119 GCTTCAATCG
*
8493129 TGAGTGTGATGCTTATAAGTACACTGATGAGGGTACTTGAGGTTTT
1 TGAGTGTGATGCTTATAAGTACACTGATAAGGGTACTTGAGGTTTT
8493175 TGAGTGTGATGCTTATAAGTACACTGATAAGGGTACTTGAGGTTTT
1 TGAGTGTGATGCTTATAAGTACACTGATAAGGGTACTTGAGGTTTT
8493221 ATTTTTTGCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.37
Consensus pattern (46 bp):
TGAGTGTGATGCTTATAAGTACACTGATAAGGGTACTTGAGGTTTT
Found at i:8499349 original size:13 final size:13
Alignment explanation
Indices: 8499331--8499369 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
8499321 TTGGCTAGTG
8499331 GACCGAAATCTTT
1 GACCGAAATCTTT
8499344 GACCGAAATCTTT
1 GACCGAAATCTTT
*
8499357 GACCTAAATCTTT
1 GACCGAAATCTTT
8499370 TACATGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (13 bp):
GACCGAAATCTTT
Found at i:8515241 original size:1 final size:1
Alignment explanation
Indices: 8515235--8515264 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
8515225 ACGGAATTAA
8515235 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
8515265 TCTTTTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:8542309 original size:9 final size:9
Alignment explanation
Indices: 8542274--8542309 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
8542264 GATATATCTC
8542274 TAAAAAAAA
1 TAAAAAAAA
*
8542283 TAAAATAAA
1 TAAAAAAAA
*
8542292 TTAAAAAAA
1 TAAAAAAAA
8542301 TAAAAAAAA
1 TAAAAAAAA
8542310 AGTTTCTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:8568409 original size:12 final size:12
Alignment explanation
Indices: 8568392--8568421 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8568382 CAGAGCTTCT
8568392 TCATCATCCTCA
1 TCATCATCCTCA
*
8568404 TCATCATCTTCA
1 TCATCATCCTCA
8568416 TCATCA
1 TCATCA
8568422 CTAACACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (12 bp):
TCATCATCCTCA
Found at i:8569240 original size:73 final size:73
Alignment explanation
Indices: 8569149--8569370 Score: 354
Period size: 73 Copynumber: 3.0 Consensus size: 73
8569139 CTTCCTGTCT
*
8569149 AAATACATTATACATTAAATTGAGCAGAAAACCAAAGGTAACAACATAACCGACAACATGCTTTA
1 AAATACATTATACATTAAATTGAGCAGAAAACCAAAGGTAACAACATAACCGAAAACATGCTTTA
8569214 ATACCCTA
66 ATACCCTA
* * * * * **
8569222 AAATACACTATGCATTAAATTGAGCAGCAAACCAAAGGCAACAACATAACCGAAAACATCCTTCG
1 AAATACATTATACATTAAATTGAGCAGAAAACCAAAGGTAACAACATAACCGAAAACATGCTTTA
8569287 ATACCCTA
66 ATACCCTA
*
8569295 AAATACATTATACATTAAATTGAGCAGAAAACCAAAGGTAACAACATTACCGAAAACATGCTTTA
1 AAATACATTATACATTAAATTGAGCAGAAAACCAAAGGTAACAACATAACCGAAAACATGCTTTA
*
8569360 CTACCCTA
66 ATACCCTA
8569368 AAA
1 AAA
8569371 CTTATGCATA
Statistics
Matches: 132, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 132 1.00
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (73 bp):
AAATACATTATACATTAAATTGAGCAGAAAACCAAAGGTAACAACATAACCGAAAACATGCTTTA
ATACCCTA
Found at i:8570298 original size:26 final size:24
Alignment explanation
Indices: 8570251--8570310 Score: 93
Period size: 26 Copynumber: 2.4 Consensus size: 24
8570241 TTACAAGCCC
8570251 AAAATAATTTTTTATTAATATTAAT
1 AAAAT-ATTTTTTATTAATATTAAT
8570276 AAAATATTTTTGGTATTAATATTAAT
1 AAAATATTTTT--TATTAATATTAAT
8570302 AAAATATTT
1 AAAATATTT
8570311 CCTTTTGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.18
25 5 0.15
26 22 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AAAATATTTTTTATTAATATTAAT
Found at i:8575159 original size:57 final size:57
Alignment explanation
Indices: 8575096--8575272 Score: 189
Period size: 57 Copynumber: 3.1 Consensus size: 57
8575086 GTATTAATAT
* * *
8575096 ATACGTGTCCGAATCT-TCTCTATTAAGTAAAAAATCATATATTAATTATTAAATTAA
1 ATACGTGTCCGAATATAT-TCTTTTAAGTAAAAAATCATATATTAATTATTAAATCAA
** * * * *
8575153 ATACGTGTTTGAATATATTTTTTTTAAGTAAAAAATCATACACTAATTATTGAATCAA
1 ATACGTGTCCGAATATA-TTCTTTTAAGTAAAAAATCATATATTAATTATTAAATCAA
* * *
8575211 ATA--TGTACTCGAATATATTCTTTTAAGTAAAAAATCATATATTAATCATTGAACCAA
1 ATACGTGT-C-CGAATATATTCTTTTAAGTAAAAAATCATATATTAATTATTAAATCAA
8575268 ATACG
1 ATACG
8575273 CGTTACCATG
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.03
57 51 0.52
58 43 0.44
59 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (57 bp):
ATACGTGTCCGAATATATTCTTTTAAGTAAAAAATCATATATTAATTATTAAATCAA
Found at i:8575183 original size:58 final size:57
Alignment explanation
Indices: 8575118--8575272 Score: 193
Period size: 58 Copynumber: 2.7 Consensus size: 57
8575108 ATCTTCTCTA
* ** * *
8575118 TTAAGTAAAAAATCATATATTAATTATTAAATTAAATACGTGTTTGAATATATTTTTT
1 TTAAGTAAAAAATCATATATTAATTATTAAATCAAATACGTACTCGAATATA-TTCTT
* * * *
8575176 TTAAGTAAAAAATCATACACTAATTATTGAATCAAATATGTACTCGAATATATTCTT
1 TTAAGTAAAAAATCATATATTAATTATTAAATCAAATACGTACTCGAATATATTCTT
* * *
8575233 TTAAGTAAAAAATCATATATTAATCATTGAACCAAATACG
1 TTAAGTAAAAAATCATATATTAATTATTAAATCAAATACG
8575273 CGTTACCATG
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 39 0.47
58 44 0.53
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (57 bp):
TTAAGTAAAAAATCATATATTAATTATTAAATCAAATACGTACTCGAATATATTCTT
Found at i:8582886 original size:33 final size:30
Alignment explanation
Indices: 8582816--8582895 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
8582806 CAGGAGGCTC
* *
8582816 ATCAGGTGGTGGTGGAGGAACCTGTTCATT
1 ATCAGGAGGAGGTGGAGGAACCTGTTCATT
* *
8582846 ATCAGGAGGAGGTGGTGGAACTTGTTCATT
1 ATCAGGAGGAGGTGGAGGAACCTGTTCATT
8582876 ATCAGGAGGAGGTGGAGGAA
1 ATCAGGAGGAGGTGGAGGAA
8582896 TCCACTCCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.25, C:0.10, G:0.40, T:0.25
Consensus pattern (30 bp):
ATCAGGAGGAGGTGGAGGAACCTGTTCATT
Found at i:8587716 original size:2 final size:2
Alignment explanation
Indices: 8587700--8587740 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
8587690 TTGCTTCACC
* *
8587700 TA TA TA AA TA AA 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
8587741 GAACAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:8590041 original size:21 final size:21
Alignment explanation
Indices: 8590017--8590056 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
8590007 ATTAATTAAT
8590017 TAAATTGAAATAT-AAAAATGG
1 TAAATTGAAAT-TGAAAAATGG
8590038 TAAATTGAAATTGAAAAAT
1 TAAATTGAAATTGAAAAAT
8590057 AAATAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
TAAATTGAAATTGAAAAATGG
Found at i:8594329 original size:14 final size:13
Alignment explanation
Indices: 8594303--8594341 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
8594293 ACGCCTTTCC
8594303 TTTTTATTTTTATT
1 TTTTTA-TTTTATT
8594317 TTATTTATTTTATT
1 TT-TTTATTTTATT
*
8594331 TTTTTAATTTA
1 TTTTTATTTTA
8594342 CGAACTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 8 0.35
14 11 0.48
15 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:8594757 original size:29 final size:29
Alignment explanation
Indices: 8594725--8594803 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
8594715 TTTATAAAGT
8594725 AAAAT-TATAAAACTTTTAAAA-AATAAAAA
1 AAAATATATAAAA-TTTTAAAATAA-AAAAA
* *
8594754 AAAATCT-TAAAATTTTAAAATAAAACAA
1 AAAATATATAAAATTTTAAAATAAAAAAA
**
8594782 AAAATATATAATTTTTTAAAAT
1 AAAATATATAAAATTTTAAAAT
8594804 TTTGAAAGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 18 0.42
29 24 0.56
30 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATATATAAAATTTTAAAATAAAAAAA
Found at i:8594794 original size:27 final size:28
Alignment explanation
Indices: 8594725--8594796 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
8594715 TTTATAAAGT
*
8594725 AAAATTATAAAACTTTTAAAAAATAAAAA
1 AAAATCATAAAA-TTTTAAAAAATAAAAA
* *
8594754 AAAATCTTAAAATTTTAAAATAA-AACAA
1 AAAATCATAAAATTTTAAAA-AATAAAAA
*
8594782 AAAAT-ATATAATTTT
1 AAAATCATAAAATTTT
8594797 TTAAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 8 0.22
28 17 0.46
29 12 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAATCATAAAATTTTAAAAAATAAAAA
Found at i:8594910 original size:21 final size:22
Alignment explanation
Indices: 8594886--8594944 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
8594876 TGTTGAAGAT
8594886 ATATTT-TAAATTAAAAATATA
1 ATATTTATAAATTAAAAATATA
** *
8594907 ATATTTATATTTTTTAAAATATA
1 ATATTTATA-AATTAAAAATATA
*
8594930 ATATTTAAAAATTAA
1 ATATTTATAAATTAA
8594945 TTATTAATAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 6 0.21
22 5 0.17
23 18 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTTATAAATTAAAAATATA
Found at i:8595141 original size:3 final size:3
Alignment explanation
Indices: 8595133--8595161 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8595123 GTAAATAGTG
8595133 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
8595162 TAAAATGAAC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:8598365 original size:146 final size:147
Alignment explanation
Indices: 8598090--8598460 Score: 471
Period size: 146 Copynumber: 2.5 Consensus size: 147
8598080 GGTGAGAGTT
*
8598090 TGAATCCATATGCCATGCAAGCTTGAATCCGGGTGAAAGTAATTGATCAAAGGGTACTCCCATTG
1 TGAATCC--ATGCCATGCAAGTTTGAATCCGGGTGAAAGT-ATTGATC-AAGGGTACTCCCATTG
* *
8598155 TCCTCCCATGCAAATTTAAAAATATTTAAACATGGAGAAACCATCTAGCAGATATCAAAACCAGG
62 TCCTCCCATGCAAATTGAAAAATATTTAAACAGGGAGAAACCATCTAGCAGATATCAAAACCAGG
* * *
8598220 TTGTTGTTCTTTATAAGAAG-
127 TTGTTGGTCTTCAGAAGAAGA
* *
8598240 TGAATCCATGCCATGCAAGTTTGTATCCGGGT-AAAGTATTCGATCAATGGGTACTCCCATTGCC
1 TGAATCCATGCCATGCAAGTTTGAATCCGGGTGAAAGTATT-GATCAA-GGGTACTCCCATTGTC
* * ** *
8598304 CTCTCATGCAAGA-TGAAACAT-TTTAAACAGGGAGAAACTGTGTAGCAGATATCAAAACCAGGT
64 CTCCCATGCAA-ATTGAAAAATATTTAAACAGGGAGAAACCATCTAGCAGATATCAAAACCAGGT
8598367 TGTTGGTCTTCAGAAGAAGAAA
128 TGTTGGTCTTCAGAAGAAG--A
* * *
8598389 TGAATCCATGCCATGCAAGTTTGAATCCAGGTGGAAGTATTTGATCGAAGGGTACTTCCATTGTC
1 TGAATCCATGCCATGCAAGTTTGAATCCGGGTGAAAGTA-TTGATC-AAGGGTACTCCCATTGTC
8598454 CTCCCAT
64 CTCCCAT
8598461 TTAATCCGGG
Statistics
Matches: 193, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
146 59 0.31
147 40 0.21
148 24 0.12
149 30 0.16
150 36 0.19
151 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (147 bp):
TGAATCCATGCCATGCAAGTTTGAATCCGGGTGAAAGTATTGATCAAGGGTACTCCCATTGTCCT
CCCATGCAAATTGAAAAATATTTAAACAGGGAGAAACCATCTAGCAGATATCAAAACCAGGTTGT
TGGTCTTCAGAAGAAGA
Found at i:8619709 original size:48 final size:48
Alignment explanation
Indices: 8619654--8619751 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
8619644 TATTTGGAAT
* *
8619654 AAGTCACATAAAGCTCAAAACTTCACACCCCATGTCTCTTTAGTGTTC
1 AAGTCACACAAAGCTCAAAACTTCACACCCCATGTCTCCTTAGTGTTC
*
8619702 AAGTCACACAAAGCTCAAAAGTTCACACCCCATGTCTCCTTAGTGTTC
1 AAGTCACACAAAGCTCAAAACTTCACACCCCATGTCTCCTTAGTGTTC
8619750 AA
1 AA
8619752 ATCATAACCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.27
Consensus pattern (48 bp):
AAGTCACACAAAGCTCAAAACTTCACACCCCATGTCTCCTTAGTGTTC
Found at i:8629304 original size:4 final size:4
Alignment explanation
Indices: 8629295--8629322 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
8629285 CATGCCCCCT
8629295 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
8629323 CTGGATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:8635704 original size:24 final size:22
Alignment explanation
Indices: 8635654--8635705 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
8635644 AAAAGAATTA
*
8635654 AATTAAATTAAAATATTTTTTT
1 AATTGAATTAAAATATTTTTTT
8635676 AATTGAATTAAAAATATATATTTTT
1 AATTGAATT-AAAATAT-T-TTTTT
8635701 -ATTGA
1 AATTGA
8635706 GTATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 8 0.31
23 7 0.27
24 6 0.23
25 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
AATTGAATTAAAATATTTTTTT
Found at i:8648647 original size:16 final size:16
Alignment explanation
Indices: 8648626--8648657 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8648616 AACAAACTTT
8648626 ATATGTTCTCTGCAGA
1 ATATGTTCTCTGCAGA
*
8648642 ATATGTTCTTTGCAGA
1 ATATGTTCTCTGCAGA
8648658 TGAGACGAGG
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:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (16 bp):
ATATGTTCTCTGCAGA
Found at i:8656481 original size:15 final size:15
Alignment explanation
Indices: 8656461--8656489 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8656451 GGGTCAAGTG
8656461 ATGAGGAAGTTCAAC
1 ATGAGGAAGTTCAAC
8656476 ATGAGGAAGTTCAA
1 ATGAGGAAGTTCAA
8656490 GTTCGACGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (15 bp):
ATGAGGAAGTTCAAC
Found at i:8670904 original size:12 final size:12
Alignment explanation
Indices: 8670869--8670906 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
8670859 GAGCGTCGAA
*
8670869 GAGAAGAAAGAG
1 GAGAAGAAAGAT
8670881 GAGAAGAAAGAT
1 GAGAAGAAAGAT
*
8670893 GAGAAAAAAGAT
1 GAGAAGAAAGAT
8670905 GA
1 GA
8670907 ATATTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (12 bp):
GAGAAGAAAGAT
Found at i:8674206 original size:12 final size:12
Alignment explanation
Indices: 8674189--8674238 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
8674179 CGTTGAAGAG
8674189 AAGAAAGAGGAA
1 AAGAAAGAGGAA
*
8674201 AAGAAAGAGGAG
1 AAGAAAGAGGAA
*
8674213 AAGAAAGATGAGA
1 AAGAAAGAGGA-A
*
8674226 AA-AAAGATGAA
1 AAGAAAGAGGAA
8674237 AA
1 AA
8674239 AATTCGAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 3 0.09
12 29 0.85
13 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (12 bp):
AAGAAAGAGGAA
Found at i:8682720 original size:22 final size:22
Alignment explanation
Indices: 8682688--8682730 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
8682678 TAAGATTCAC
*
8682688 TCTTGATTATCTAACCAAGCAT
1 TCTTGACTATCTAACCAAGCAT
8682710 TCTTGACTATCTAACCAAGCA
1 TCTTGACTATCTAACCAAGCA
8682731 CTAACTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (22 bp):
TCTTGACTATCTAACCAAGCAT
Found at i:8690883 original size:4 final size:4
Alignment explanation
Indices: 8690874--8690911 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
8690864 ACACACCACT
8690874 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
8690912 ATTGAGTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:8695056 original size:30 final size:31
Alignment explanation
Indices: 8695020--8695086 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 31
8695010 TATAAAGATG
8695020 TATTTTAGTAAAATCTGCAAAAAAAA-TATT
1 TATTTTAGTAAAATCTGCAAAAAAAATTATT
*
8695050 TATTTTAGTAAAATCTTCAAAAAAAATTATT
1 TATTTTAGTAAAATCTGCAAAAAAAATTATT
8695081 TATTTT
1 TATTTT
8695087 GGAAAACCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (31 bp):
TATTTTAGTAAAATCTGCAAAAAAAATTATT
Found at i:8718281 original size:18 final size:18
Alignment explanation
Indices: 8718241--8718285 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
8718231 ATTTAAAATC
8718241 AAATCGATTAAATTAATT
1 AAATCGATTAAATTAATT
* **
8718259 TAATCGATTAAATTGGTT
1 AAATCGATTAAATTAATT
8718277 AAATCGATT
1 AAATCGATT
8718286 GAATAAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (18 bp):
AAATCGATTAAATTAATT
Found at i:8720276 original size:59 final size:59
Alignment explanation
Indices: 8720184--8720304 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
8720174 CATAGAAAGA
* *
8720184 ACAACTAGATCCAACTCTGGGTCCTCTCCTCTAAGTCTGCCGCATCTGCATGCATGGTG
1 ACAACTAGATCCAACTCTGGGTCCTCTCATCTAAGTCTGCCGCATCTGCATGCATAGTG
* *
8720243 ACAACTATATCCAACTCTGGGTCCTCTCATCTAAGTCTGCTGCATCTGCATGCATAGTG
1 ACAACTAGATCCAACTCTGGGTCCTCTCATCTAAGTCTGCCGCATCTGCATGCATAGTG
8720302 ACA
1 ACA
8720305 GGTACGTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (59 bp):
ACAACTAGATCCAACTCTGGGTCCTCTCATCTAAGTCTGCCGCATCTGCATGCATAGTG
Found at i:8725853 original size:586 final size:587
Alignment explanation
Indices: 8724625--8725895 Score: 1464
Period size: 586 Copynumber: 2.2 Consensus size: 587
8724615 TGAGTTTAGA
** * * *
8724625 TTTATGATTATAGTTTTTGTTGAAGTTGAACTTGAAAACTCAAATTTAAAAGAAGAGATATAAAT
1 TTTATGATTATAGTTTTCATTTAGGTTGAACTTGAAAACTTAAATTTAAAAG-AGAGATATAAAT
* * * ** *
8724690 TTGAAATGTAATATAAATGTGAATGATAAGGCCATTTGTCCATTTTGTTCAAGCGTATTCATAAT
65 TTCAAATGTAATAT-AATGTGAATGATAAGGCCATTTGACCATTTGGCCCAAGCGAATTCATAAT
* *
8724755 CATGTCTTTCCAAACATGCATGGACTAGTATTTAATGAATAAGCATCAACCAACATAATTAATGA
129 CATGTCTTTCCAAACATGCATGGACTAGTATTTAAAGAATAAGCATCAACCAAC--AATCAATGA
* * **
8724820 TTCAACAAATTAATTGCATTGTTTCTTTCTTAATTTGCCTTGACCCAAATATAATCTTAACAATG
192 TTCAACAAATAAATTGCAATGTTTCTTTCTTAATTTGCCTCAACCCAAATATAATCTTAACAATG
* * *
8724885 GAAAAGAAGTTCTGAATGTATATAAAAAGAGATATAGCTTTCTCAGCATATAAATTTCTAACCTT
257 GAAAAGAAGTTCTGAATATATATAAAAAGAGATATAGCTCTCTCAGAATATAAATTTCTAACCTT
* * * * * * *
8724950 CCATCCTTATGATTAATATATATCTTTATTGAAAATATTGATTTCCATACTAATAATCTCATTGC
322 CAATCCTGAAGATTAATATATATCTTTATTAAAAAAATTGATTTCAATACTAATAATATCATTGC
* * * * *
8725015 AGGTCAAATTCCATTAGCTCTATTCGAGTGCCGAGAGTTAGAAATTTTATTGTTATCTAATAATG
387 AGGTCAAATTCCATCAACTCTATTCAAGTGCCAAGAGTTAGAAATTTTATTGTTATCTAACAATG
**
8725080 CCTTGGAGGGAAGCATACCTCAAGAAATCGGGAATTTGACTAGATTAAGATTGTTGTACCTTGAT
452 CCTTGGAGGGAAGCATACCTCAAGAAATCGCAAATTTGACTAGATTAAGATTGTTGTACCTTGA-
* *
8725145 CATAACAACTTAACAGGTATGCTTAATATCAGCCTTCTTTTAGACAAATTAACGATTAGTGGACA
516 CATAACAACCTAACAGGTATGCTTAATATCAGCCTTCCTTTAGACAAATTAACGATTAGTGGACA
8725210 ATTTATT
581 ATTTATT
* **
8725217 TTTATTCGTGATT-TAGATTTATGATTCT-GGTT-TTCATTG---ACTTAAATTTAAAAG-GAGA
1 TTTA----TGATTATAG-TTT-TCATT-TAGGTTGAAC-TTGAAAACTTAAATTTAAAAGAGAGA
*
8725275 TATAAATTTCAAATGTAATATAA-GT-ACATGTGATAAGGCCATTTGACCATTTGGCCCAA-TGA
58 TATAAATTTCAAATGTAATATAATGTGA-A--TGATAAGGCCATTTGACCATTTGGCCCAAGCGA
* * *
8725337 ATTCATAA-CGATGTCTTTCGAAACATG-AGTGTACTTAGTATTTAAAGAATAAGCATCACCCAA
120 ATTCATAATC-ATGTCTTTCCAAACATGCA-TGGAC-TAGTATTTAAAGAATAAGCATCAACCAA
* *
8725400 C-A-CAATGATTCAACAAATAAATTGCAATGTTTCTTTTTTAATTTGGCTCAACCCTAAATATAA
182 CAATCAATGATTCAACAAATAAATTGCAATGTTTCTTTCTTAATTTGCCTCAACCC-AAATATAA
* *
8725463 TCTTAACAATGGAAAAGAAGTT-TTAACTATATATAAAAAGCA-ATATAGCTCTCTTAGAATATA
246 TCTTAACAATGGAAAAGAAGTTCTGAA-TATATATAAAAAG-AGATATAGCTCTCTCAGAATATA
*
8725526 AATTTCT-ACCTTCAATCCTGAAGA-TCA-ATATATCTTTATTAAAAAAATTGATTTCAATACTA
309 AATTTCTAACCTTCAATCCTGAAGATTAATATATATCTTTATTAAAAAAATTGATTTCAATACTA
* * * *
8725588 ATAATATCTTTGCAGGTCGACTTCCATCAACTCTATTCAAGTGCCAAGAGTTAGGACA-TTTATC
374 ATAATATCATTGCAGGTCAAATTCCATCAACTCTATTCAAGTGCCAAGAGTTA-GAAATTTTAT-
* *
8725652 T-TTATCTCACAATGCCTTGGAGGGAAG-AGTACCTCAAGAAATTGCAAATTTGACTAGATTAAG
437 TGTTATCTAACAATGCCTTGGAGGGAAGCA-TACCTCAAGAAATCGCAAATTTGACTAGATTAAG
* * * *
8725715 CTAT-TTGTATCTCTTTGA-A-AACATCCTAACAGGTATGCTTAATGT-TGACCTTCCTTTAGAC
501 AT-TGTTGTA-C-C-TTGACATAACAACCTAACAGGTATGCTTAATATCAG-CCTTCCTTTAGAC
*
8725776 AAATTAAAACGATTAGTTGG-CAATTTGTT
561 AAATT--AACGATTAG-TGGACAATTTATT
* *
8725805 TTTATAATTATAGTTTTCATTTAGGTTGAACTTGAAAACTTGAATTTAAAAGAAGAGACT-TAAA
1 TTTATGATTATAGTTTTCATTTAGGTTGAACTTGAAAACTTAAATTTAAAAG-AGAGA-TATAAA
*
8725869 TTTCAAATGTAATATAAATGTGGATGA
64 TTTCAAATGTAATAT-AATGTGAATGA
8725896 GTTTTGGGTG
Statistics
Matches: 575, Mismatches: 64, Indels: 84
0.80 0.09 0.12
Matches are distributed among these distances:
582 1 0.00
583 11 0.02
584 8 0.01
585 5 0.01
586 197 0.34
587 9 0.02
588 110 0.19
589 79 0.14
590 9 0.02
591 31 0.05
592 80 0.14
594 14 0.02
595 3 0.01
596 9 0.02
597 9 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (587 bp):
TTTATGATTATAGTTTTCATTTAGGTTGAACTTGAAAACTTAAATTTAAAAGAGAGATATAAATT
TCAAATGTAATATAATGTGAATGATAAGGCCATTTGACCATTTGGCCCAAGCGAATTCATAATCA
TGTCTTTCCAAACATGCATGGACTAGTATTTAAAGAATAAGCATCAACCAACAATCAATGATTCA
ACAAATAAATTGCAATGTTTCTTTCTTAATTTGCCTCAACCCAAATATAATCTTAACAATGGAAA
AGAAGTTCTGAATATATATAAAAAGAGATATAGCTCTCTCAGAATATAAATTTCTAACCTTCAAT
CCTGAAGATTAATATATATCTTTATTAAAAAAATTGATTTCAATACTAATAATATCATTGCAGGT
CAAATTCCATCAACTCTATTCAAGTGCCAAGAGTTAGAAATTTTATTGTTATCTAACAATGCCTT
GGAGGGAAGCATACCTCAAGAAATCGCAAATTTGACTAGATTAAGATTGTTGTACCTTGACATAA
CAACCTAACAGGTATGCTTAATATCAGCCTTCCTTTAGACAAATTAACGATTAGTGGACAATTTA
TT
Found at i:8732333 original size:2 final size:2
Alignment explanation
Indices: 8732326--8732373 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
8732316 GTATGATCAT
8732326 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
8732368 TA TA TA
1 TA TA TA
8732374 GTGTTGTGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8745503 original size:17 final size:17
Alignment explanation
Indices: 8745464--8745509 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
8745454 AAAGAATTTG
8745464 ATCAAAGAAAAAATATTA
1 ATCAAAGAAAAAATA-TA
8745482 A-CAAAGAAATAAATA-A
1 ATCAAAGAAA-AAATATA
8745498 ATCAAAAGAAAA
1 ATC-AAAGAAAA
8745510 TGCATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.08
17 10 0.40
18 13 0.52
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.15
Consensus pattern (17 bp):
ATCAAAGAAAAAATATA
Found at i:8745524 original size:2 final size:2
Alignment explanation
Indices: 8745517--8745548 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8745507 AAATGCATTA
8745517 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
8745549 GAAACTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8763955 original size:2 final size:2
Alignment explanation
Indices: 8763948--8763993 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
8763938 ATTTAATAGA
8763948 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG A- AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8763988 -G AG AG A
1 AG AG AG A
8763994 CCGGCGCGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8765054 original size:18 final size:17
Alignment explanation
Indices: 8765031--8765085 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
8765021 AATCTAGATA
8765031 AATAAAAAATAAACAAAT
1 AATAAAAAATAAA-AAAT
8765049 AATAAAAATAATAAAAAAT
1 AAT-AAAA-AATAAAAAAT
*
8765068 -ATAAAGACATAAAAAAT
1 AATAAA-AAATAAAAAAT
8765085 A
1 A
8765086 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 12 0.38
18 6 0.19
19 8 0.25
20 6 0.19
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (17 bp):
AATAAAAAATAAAAAAT
Found at i:8778443 original size:2 final size:2
Alignment explanation
Indices: 8778436--8778470 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8778426 CTGTAATCAT
8778436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8778471 TGTGGTGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8784883 original size:24 final size:24
Alignment explanation
Indices: 8784856--8784902 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
8784846 TACATAAATT
8784856 AAAA-TAAATTGTGAATTCAACTTG
1 AAAATTAAATT-TGAATTCAACTTG
* *
8784880 AAAATTTAATTTGAATTTAACTT
1 AAAATTAAATTTGAATTCAACTT
8784903 AATTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (24 bp):
AAAATTAAATTTGAATTCAACTTG
Found at i:8816345 original size:6 final size:6
Alignment explanation
Indices: 8816336--8816361 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8816326 ACCACTCCTT
8816336 CCAAAC CCAAAC CCAAAC CCAAAC CC
1 CCAAAC CCAAAC CCAAAC CCAAAC CC
8816362 GAAGATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.54, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAC
Found at i:8824232 original size:2 final size:2
Alignment explanation
Indices: 8824225--8824268 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
8824215 ATTAAGATGA
* * *
8824225 AT AT AT AT AT AT AT AT AT AT AT AT CT CT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8824267 AT
1 AT
8824269 CGGCATGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8825246 original size:9 final size:9
Alignment explanation
Indices: 8825205--8825257 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
8825195 CTTGTTTTTT
8825205 CATATGAAA
1 CATATGAAA
8825214 CATATTAGTAATA
1 CATA-T-G-AA-A
*
8825227 CTTAT-AAA
1 CATATGAAA
8825235 CATATGAAA
1 CATATGAAA
8825244 CATATGAAA
1 CATATGAAA
8825253 CATAT
1 CATAT
8825258 AAGTAGTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 5 0.14
9 23 0.62
10 1 0.03
11 1 0.03
12 3 0.08
13 4 0.11
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (9 bp):
CATATGAAA
Found at i:8832558 original size:17 final size:18
Alignment explanation
Indices: 8832523--8832558 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8832513 CGCGGCGAGG
*
8832523 GGGCCCCGGCGCGCGGAC
1 GGGCCCCGGCGCGCCGAC
8832541 GGGCCCCGG-GCGCCGAC
1 GGGCCCCGGCGCGCCGAC
8832558 G
1 G
8832559 CCCGCCGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.06, C:0.44, G:0.50, T:0.00
Consensus pattern (18 bp):
GGGCCCCGGCGCGCCGAC
Found at i:8832647 original size:16 final size:17
Alignment explanation
Indices: 8832607--8832650 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
8832597 GCCGTGCCGG
*
8832607 CCGCGCGGCGCCGGCGC
1 CCGCGCGGCGCCCGCGC
8832624 CCGCCGCGGCGCCCGC-C
1 CCG-CGCGGCGCCCGCGC
8832641 CCGCGCGGCG
1 CCGCGCGGCG
8832651 GCGCGGCGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 7 0.28
18 11 0.44
ACGTcount: A:0.00, C:0.57, G:0.43, T:0.00
Consensus pattern (17 bp):
CCGCGCGGCGCCCGCGC
Found at i:8832679 original size:36 final size:34
Alignment explanation
Indices: 8832607--8832687 Score: 87
Period size: 36 Copynumber: 2.4 Consensus size: 34
8832597 GCCGTGCCGG
*
8832607 CCGCGCGGCGCCGGCGCCCGCCGCGGCGCCCGCC
1 CCGCGCGGCGCCGGCGCCCGCCGCGGCGCCCCCC
* *
8832641 CCGCGCGGCGGCGCGGCGGCCGCCTC-GCGCACCCCC
1 CCGCGCGGC-GC-CGGCGCCCGCCGCGGCGC-CCCCC
8832677 CCG-G-GGCGCCG
1 CCGCGCGGCGCCG
8832688 CCGCGGGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
32 2 0.05
33 2 0.05
34 12 0.29
35 7 0.17
36 18 0.44
ACGTcount: A:0.01, C:0.56, G:0.42, T:0.01
Consensus pattern (34 bp):
CCGCGCGGCGCCGGCGCCCGCCGCGGCGCCCCCC
Found at i:8835369 original size:17 final size:16
Alignment explanation
Indices: 8835340--8835373 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
8835330 TAACATAATG
8835340 ATTAAATATATAAATA
1 ATTAAATATATAAATA
8835356 ATTAAATAATATAAATA
1 ATTAAAT-ATATAAATA
8835373 A
1 A
8835374 AAAAGCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAATATATAAATA
Found at i:8849797 original size:18 final size:18
Alignment explanation
Indices: 8849774--8849809 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
8849764 TATTAAGTGA
8849774 AAAAGAAG-GAAAAGAATG
1 AAAAGAAGAGAAAA-AATG
8849792 AAAAGAAGAGAAAAAATG
1 AAAAGAAGAGAAAAAATG
8849810 TTGTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAGAAAAAATG
Found at i:8852213 original size:98 final size:98
Alignment explanation
Indices: 8852044--8852241 Score: 353
Period size: 98 Copynumber: 2.0 Consensus size: 98
8852034 AATATAATGA
8852044 ATCAGATGGAACAGCAACTTAAATTTTCTCAAGACAGTTTGAGAGTTCGACGTCAATTGAAAAAA
1 ATCAGATGGAACAGCAACTTAAATTTTCTCAAGACAGTTTGAGAGTTCGACGTCAATTGAAAAAA
*
8852109 CAAAAAGATCGCACTAGTTCACAGAGAAACAAT
66 CAAAAAGATCACACTAGTTCACAGAGAAACAAT
*
8852142 ATCAGATGGAACAGCAAC-TAAATTTTTCTCAAGACAGTTTGAGAGTTCGACGTCAATTTAAAAA
1 ATCAGATGGAACAGCAACTTAAA-TTTTCTCAAGACAGTTTGAGAGTTCGACGTCAATTGAAAAA
*
8852206 ACAAAAAGATCACACTAGTTCACGGAGAAACAAT
65 ACAAAAAGATCACACTAGTTCACAGAGAAACAAT
8852240 AT
1 AT
8852242 GTATCTCAGA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 4 0.04
98 92 0.96
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (98 bp):
ATCAGATGGAACAGCAACTTAAATTTTCTCAAGACAGTTTGAGAGTTCGACGTCAATTGAAAAAA
CAAAAAGATCACACTAGTTCACAGAGAAACAAT
Done.