Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 33
Found at i:5442534 original size:17 final size:19
Alignment explanation
Indices: 5442492--5442529 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5442482 TTGGACCCTT
*
5442492 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
*
5442511 AGTGCATCGATGCATTAAG
1 AGTGCATCGATGCACTAAG
5442530 TGCATTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:5442647 original size:66 final size:65
Alignment explanation
Indices: 5442512--5442672 Score: 202
Period size: 66 Copynumber: 2.5 Consensus size: 65
5442502 TGCACTAAGA
* * * *
5442512 GTGCATCGATGCATTAAGTGCATTCGATG--TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCAAAATAGCCACAGTGCATCGATGCATGGAT
* * *
5442575 GATGCATCGATGCATCAAATGCATTCGATGTTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 G-TGCATCGATGCATCAAATGCATTCGATGTTTTTCA-AAATAGCCACAGTGCATCGATGCATGG
5442639 TAT
64 -AT
*
5442642 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
5442673 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 26 0.31
66 53 0.62
67 5 0.06
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTTCAAAATAGCCACAGTGCATCGATGCATGGAT
Found at i:5445344 original size:23 final size:22
Alignment explanation
Indices: 5445314--5445379 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
5445304 CATGACCTTT
5445314 ATGCATCGATGCATATTCAAGG
1 ATGCATCGATGCATATTCAAGG
* * * *
5445336 AATGCATCGGTGCATCTT-TATG
1 -ATGCATCGATGCATATTCAAGG
*
5445358 ATGCATCGATGCACATTCAAGG
1 ATGCATCGATGCATATTCAAGG
5445380 GGATGTCAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 14 0.42
22 4 0.12
23 15 0.45
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (22 bp):
ATGCATCGATGCATATTCAAGG
Found at i:5450590 original size:17 final size:19
Alignment explanation
Indices: 5450548--5450585 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5450538 TTGGACCCTT
*
5450548 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
*
5450567 AGTGCATCGATGCATTAAG
1 AGTGCATCGATGCACTAAG
5450586 TGCATTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:5450705 original size:67 final size:66
Alignment explanation
Indices: 5450568--5450729 Score: 197
Period size: 67 Copynumber: 2.5 Consensus size: 66
5450558 TGCACTAAGA
* * *
5450568 GTGCATCGATGCATTAAGTGCATTCGATG--TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
5450631 G
66 G
* * *
5450632 GTGCATCGATGCATCAAATGCATTCGATGTTTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTTTCA-AAATAGCCACAGTGCATCGATGCATGG
*
5450696 -TAT
64 CT-G
*
5450699 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
5450730 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
64 27 0.32
66 3 0.04
67 52 0.61
68 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (66 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
G
Found at i:5451312 original size:6 final size:6
Alignment explanation
Indices: 5451301--5451439 Score: 56
Period size: 6 Copynumber: 22.3 Consensus size: 6
5451291 ACTATTTATA
* *
5451301 ATTAAT ATTAAT A-TAA- ATTCTAT ATT-AT AATTAAT ATTATTAT AATTATT
1 ATTAAT ATTAAT ATTAAT ATT-AAT ATTAAT -ATTAAT ATTA--AT -ATTAAT
* * *
5451351 ATTAAT ATTAA- ATT-AT ATTAAT ATAATAT AGTTTAT AATTTAT AATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTA-AT A-TTAAT -ATTAAT -ATTAAT
* * * *
5451401 ATTAAT A-TAAA ATATAGT CTATAAA ATTAAT ATTAAT AT
1 ATTAAT ATTAAT AT-TAAT AT-TAAT ATTAAT ATTAAT AT
5451440 AAACTATAGT
Statistics
Matches: 103, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
4 2 0.02
5 16 0.16
6 48 0.47
7 29 0.28
8 4 0.04
9 4 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:5451325 original size:50 final size:46
Alignment explanation
Indices: 5451270--5451411 Score: 130
Period size: 50 Copynumber: 3.0 Consensus size: 46
5451260 TAATTTCATC
*
5451270 CTATATAATTTATATTAATAAACTATTTATAATTAATATTAATATAAATT
1 CTATATAATATA-ATTAAT--A-TATTTATAATTAATATTAATATAAATT
*
5451320 CTATAT--TATAATTAATAT-TATTATAATTATTATTAATATTAAATT
1 CTATATAATATAATTAATATAT-TTATAATTAATATTAATA-TAAATT
* *
5451365 ATAT-TAATATAATATAGTTTATAATTTATAATTAATATTAATATAAA
1 CTATATAATATAAT-TA--ATAT-ATTTATAATTAATATTAATATAAA
5451412 ATATAGTCTA
Statistics
Matches: 78, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
43 1 0.01
44 19 0.24
45 10 0.13
46 6 0.08
47 8 0.10
48 3 0.04
49 7 0.09
50 23 0.29
51 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (46 bp):
CTATATAATATAATTAATATATTTATAATTAATATTAATATAAATT
Found at i:5451346 original size:44 final size:48
Alignment explanation
Indices: 5451294--5451416 Score: 146
Period size: 44 Copynumber: 2.6 Consensus size: 48
5451284 TTAATAAACT
* * *
5451294 ATTTATAATTAATATTAATATAAATTCTA-TATTATAAT-TA-ATATT
1 ATTTATAATTAATATTAATATAAATTATATTAATATAATATAGATATA
* *
5451339 A-TTATAATTATTATTAATATTAAATTATATTAATATAATATAGTTTATA
1 ATTTATAATTAATATTAATA-TAAATTATATTAATATAATATAG-ATATA
*
5451388 ATTTATAATTAATATTAATATAAAATATA
1 ATTTATAATTAATATTAATATAAATTATA
5451417 GTCTATAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
44 17 0.26
45 9 0.14
46 8 0.12
47 2 0.03
49 12 0.18
50 17 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (48 bp):
ATTTATAATTAATATTAATATAAATTATATTAATATAATATAGATATA
Found at i:5451371 original size:16 final size:18
Alignment explanation
Indices: 5451322--5451408 Score: 73
Period size: 16 Copynumber: 5.2 Consensus size: 18
5451312 TATAAATTCT
5451322 ATATTATAATTA--A-TA
1 ATATTATAATTATTATTA
*
5451337 TTATTATAATTATTATTA
1 ATATTATAATTATTATTA
5451355 ATATTA-AATTA-TATTA
1 ATATTATAATTATTATTA
* *
5451371 ATATAATATAGT-TTA-TA
1 ATATTATA-ATTATTATTA
*
5451388 AT-TTATAATTAATATTA
1 ATATTATAATTATTATTA
5451405 ATAT
1 ATAT
5451409 AAAATATAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
15 13 0.23
16 16 0.29
17 15 0.27
18 12 0.21
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (18 bp):
ATATTATAATTATTATTA
Found at i:5451424 original size:36 final size:35
Alignment explanation
Indices: 5451402--5451540 Score: 93
Period size: 31 Copynumber: 4.2 Consensus size: 35
5451392 ATAATTAATA
*
5451402 TTAATATAAAATATAGTCTAT-A--A-AATTAATA
1 TTAATATAAAATATAGTTTATAATTATAATTAATA
* *
5451433 TTAATATAAACTATAGTTTATAAATTATATAGT-ATA
1 TTAATATAAAATATAGTTTAT-AATTATA-ATTAATA
*
5451469 GTT--TATAAACTATAG--T-TAA-TATAATTAATA
1 -TTAATATAAAATATAGTTTATAATTATAATTAATA
** * *
5451499 TTAATATAGTATATGGTTTATAGACTATAATTAATA
1 TTAATATAAAATATAGTTTATA-ATTATAATTAATA
5451535 TTAATA
1 TTAATA
5451541 CTATATACTA
Statistics
Matches: 85, Mismatches: 8, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
29 4 0.05
30 7 0.08
31 29 0.34
32 1 0.01
33 3 0.04
34 2 0.02
35 14 0.16
36 21 0.25
37 4 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (35 bp):
TTAATATAAAATATAGTTTATAATTATAATTAATA
Found at i:5451432 original size:31 final size:30
Alignment explanation
Indices: 5451394--5451506 Score: 120
Period size: 31 Copynumber: 3.5 Consensus size: 30
5451384 TATAATTTAT
*
5451394 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
5451425 AATTAATATTAATATAAACTATAGTT-TATA
1 AATTAATATTAATATAAACTATAGTTATA-A
* *
5451455 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAACTATAGTT-ATAA
5451491 AATTAATATTAATATA
1 AATTAATATTAATATA
5451507 GTATATGGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
29 2 0.03
30 7 0.10
31 31 0.44
32 1 0.01
33 4 0.06
34 1 0.01
35 17 0.24
36 5 0.07
37 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:5451446 original size:24 final size:25
Alignment explanation
Indices: 5451401--5451447 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5451391 TATAATTAAT
**
5451401 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
5451426 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
5451448 GTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:5451518 original size:66 final size:64
Alignment explanation
Indices: 5451297--5451537 Score: 198
Period size: 66 Copynumber: 3.8 Consensus size: 64
5451287 ATAAACTATT
* * *
5451297 TATAATTAATATTAATATAA-AT--TCTAT--ATTATAATTAATATTAT-TATAATTATTA-TTA
1 TATAATTAATATTAATATAATATAGTTTATAAATTATAAGTAATATTATATA-AAATA-TAGTTA
5451355 A
64 A
* *
5451356 TATTAAATT-ATATTAATATAATATAGTTTATAATTTATAATTAATATTAATATAAAATATAGTC
1 TA-T-AATTAATATTAATATAATATAGTTTATAAATTATAAGTAATATT-ATATAAAATATAGT-
5451420 T-A
62 TAA
* *
5451422 TAAAATTAATATTAATATAAACTATAGTTTATAAATTATATAGT-ATAGTT-TATAAACTATAGT
1 TATAATTAATATTAATAT-AA-TATAGTTTATAAATTATA-AGTAATA-TTATATAAAATATAGT
5451485 TAA
62 TAA
* * * *
5451488 TATAATTAATATTAATATAGTATATGGTTTATAGACTATAATTAATATTA
1 TATAATTAATATTAATATA--ATATAGTTTATAAATTATAAGTAATATTA
5451538 ATACTATATA
Statistics
Matches: 149, Mismatches: 12, Indels: 35
0.76 0.06 0.18
Matches are distributed among these distances:
59 2 0.01
60 13 0.09
61 6 0.04
63 4 0.03
64 4 0.03
65 32 0.21
66 60 0.40
67 24 0.16
68 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (64 bp):
TATAATTAATATTAATATAATATAGTTTATAAATTATAAGTAATATTATATAAAATATAGTTAA
Found at i:5451565 original size:15 final size:17
Alignment explanation
Indices: 5451532--5451575 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
5451522 ACTATAATTA
5451532 ATATTAATACTATATACT
1 ATATTAATA-TATATACT
5451550 ATATTAATATA-A-ACT
1 ATATTAATATATATACT
5451565 ATATTTAATAT
1 ATA-TTAATAT
5451576 GTTAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 2 0.08
18 9 0.36
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAATATATATACT
Found at i:5451634 original size:36 final size:36
Alignment explanation
Indices: 5451594--5451672 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
5451584 TAATGTAAAC
*
5451594 TATAGTTTATAAACTATCTACTACATTAATACAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
* *
5451630 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
5451666 TATAGTT
1 TATAGTT
5451673 AAGATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TATAGTTTATAAACTATATACTACATTAATACAAAT
Found at i:5451669 original size:15 final size:15
Alignment explanation
Indices: 5451651--5451701 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5451641 AACTATATAC
5451651 TATATTAATATAAAT
1 TATATTAATATAAAT
*
5451666 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
5451681 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
5451697 TATAT
1 TATAT
5451702 AGTAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:5451738 original size:21 final size:21
Alignment explanation
Indices: 5451712--5451759 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
5451702 AGTAAATTAA
* *
5451712 TATATAATATAGTTTATAAAT
1 TATATAATATAGGTTATAAAC
*
5451733 TATATACTATAGGTTATAAAC
1 TATATAATATAGGTTATAAAC
5451754 TATATA
1 TATATA
5451760 GTACACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (21 bp):
TATATAATATAGGTTATAAAC
Found at i:5451823 original size:2 final size:2
Alignment explanation
Indices: 5451818--5451918 Score: 168
Period size: 2 Copynumber: 51.0 Consensus size: 2
5451808 TACATATAAT
* *
5451818 TA TA TA AA TA GA T- 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
5451859 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
*
5451901 TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
5451919 CATAGTTTAT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5451961 original size:35 final size:36
Alignment explanation
Indices: 5451920--5451993 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
5451910 ATATATATAC
*
5451920 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
5451955 ATAGTTTACATGTATACATATACTATATGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
5451992 AT
1 AT
5451994 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:5452182 original size:48 final size:45
Alignment explanation
Indices: 5452122--5452212 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
5452112 AAGATTTAGG
* *
5452122 GTTTCTATAAACTATATACTTAATTACTTTATATAGTTTATGTATAGT
1 GTTTCGATAAACTATATAC-T--TTACTTTATATAGTTTATATATAGT
*
5452170 GTTTCGATAAACTATTTACTTTACTTTATATAGTTTATATATA
1 GTTTCGATAAACTATATACTTTACTTTATATAGTTTATATATA
5452213 TATATAGGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 22 0.55
47 1 0.03
48 17 0.43
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.51
Consensus pattern (45 bp):
GTTTCGATAAACTATATACTTTACTTTATATAGTTTATATATAGT
Found at i:5452210 original size:2 final size:2
Alignment explanation
Indices: 5452205--5452252 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
5452195 TTATATAGTT
** *
5452205 TA TA TA TA TA TA TA GG T- TA TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
5452247 TA TA TA
1 TA TA TA
5452253 CTGTTGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5452235 original size:23 final size:23
Alignment explanation
Indices: 5452205--5452252 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5452195 TTATATAGTT
5452205 TATATATATATATAGGTTATATA
1 TATATATATATATAGGTTATATA
*
5452228 TATATATATATATAGTTTATATA
1 TATATATATATATAGGTTATATA
5452251 TA
1 TA
5452253 CTGTTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TATATATATATATAGGTTATATA
Found at i:5452252 original size:17 final size:17
Alignment explanation
Indices: 5452196--5452235 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5452186 TACTTTACTT
*
5452196 TATATAGTTTATATATA
1 TATATAGGTTATATATA
5452213 TATATAGGTTATATATA
1 TATATAGGTTATATATA
5452230 TATATA
1 TATATA
5452236 TATATAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAGGTTATATATA
Found at i:5452572 original size:19 final size:19
Alignment explanation
Indices: 5452548--5452586 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5452538 TCGAATGCAT
5452548 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
5452567 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
5452586 T
1 T
5452587 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:5452610 original size:64 final size:65
Alignment explanation
Indices: 5452504--5452647 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 65
5452494 TTTTCAAAGG
* **
5452504 CATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCATTCCATGCACCGATGCACTCT
1 CATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGCATTCCATGCACCGATGCACAAT
5452568 C
65 C
* * ** *
5452569 CATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAATC
1 CATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTCCATGCACCGATGCACAATC
5452633 CATGCATCGATGCAC
1 CATGCATCGATGCAC
5452648 CAGGCTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 54 0.77
65 14 0.20
66 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (65 bp):
CATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTCCATGCACCGATGCACAATC
Found at i:5452665 original size:64 final size:63
Alignment explanation
Indices: 5452533--5452688 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 63
5452523 GAATAAATTG
* * ** *
5452533 AAACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTA
1 AAACATCGAATGCATTTCATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTA
*
5452597 AAACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TT
1 AAACATCGAATGCATTTCATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATT
*
5452660 C
63 A
*
5452661 AAACATCGAATGCACTTCATGCATCGAT
1 AAACATCGAATGCATTTCATGCATCGAT
5452689 ACACTATTAG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
64 73 0.91
65 1 0.01
66 4 0.05
67 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (63 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTATTA
Found at i:5457013 original size:20 final size:21
Alignment explanation
Indices: 5456969--5457014 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
5456959 ATCGGTTCAG
*
5456969 ACCGG-TC-AAACCGGTCAAA
1 ACCGGTTCAAAACCAGTCAAA
*
5456988 ATCGGTTCAAAACCAGTC-AA
1 ACCGGTTCAAAACCAGTCAAA
5457008 ACCGGTT
1 ACCGGTT
5457015 TTCCAGCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 10 0.45
21 8 0.36
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (21 bp):
ACCGGTTCAAAACCAGTCAAA
Found at i:5464210 original size:7 final size:7
Alignment explanation
Indices: 5464198--5464222 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5464188 GGTCAAAGGA
5464198 GGTCAAC
1 GGTCAAC
5464205 GGTCAAC
1 GGTCAAC
5464212 GGTCAAC
1 GGTCAAC
5464219 GGTC
1 GGTC
5464223 GGGTCGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:5464294 original size:20 final size:20
Alignment explanation
Indices: 5464257--5464299 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5464247 GGTTCAGACC
*
5464257 GTTCAAACCGGTCAAAACTG
1 GTTCAAACCGGTCAAAACCG
5464277 GTTCAAAACCGGTC-AAACCG
1 GTTC-AAACCGGTCAAAACCG
5464297 GTT
1 GTT
5464300 TTCCTACTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
GTTCAAACCGGTCAAAACCG
Found at i:5464297 original size:9 final size:10
Alignment explanation
Indices: 5464261--5464298 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
5464251 CAGACCGTTC
5464261 AAACCGGTCA
1 AAACCGGTCA
*
5464271 AAACTGGTTCA
1 AAACCGG-TCA
5464282 AAACCGGTC-
1 AAACCGGTCA
5464291 AAACCGGT
1 AAACCGGT
5464299 TTTCCTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (10 bp):
AAACCGGTCA
Found at i:5474490 original size:19 final size:19
Alignment explanation
Indices: 5474466--5474504 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5474456 TCGAATGCAT
5474466 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
5474485 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
5474504 T
1 T
5474505 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:5474529 original size:64 final size:65
Alignment explanation
Indices: 5474401--5474565 Score: 201
Period size: 64 Copynumber: 2.5 Consensus size: 65
5474391 TTTTCAAAGG
*
5474401 CATGCACCGATGCA-TCCATGCCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACT-C-T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGC
5474464 ATTC
62 ATTC
* * *
5474468 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * **
5474532 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCAC
5474566 CAGGCTAGTT
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 54 0.61
65 15 0.17
66 3 0.03
67 15 0.17
68 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:5475383 original size:35 final size:36
Alignment explanation
Indices: 5475343--5475416 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
5475333 TATACTATAC
*
5475343 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
5475378 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
5475415 AT
1 AT
5475417 TAACTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:5475659 original size:28 final size:27
Alignment explanation
Indices: 5475625--5475678 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
5475615 TATACTTTTT
*
5475625 ATAGTTTATACATATATAGTTTATATAC
1 ATAGTTTATACATATATA-TATATATAC
*
5475653 ATAGTTTATATATATATATATATATA
1 ATAGTTTATACATATATATATATATA
5475679 GTTCATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
ATAGTTTATACATATATATATATATAC
Found at i:5475693 original size:38 final size:36
Alignment explanation
Indices: 5475587--5475706 Score: 134
Period size: 38 Copynumber: 3.2 Consensus size: 36
5475577 ATACATACAC
*
5475587 ATATATATATAT-TATAGTTTATAAACTATATACTTTTT
1 ATATATATATATATATAGTTTATAAAC-ATA-A-TTTAT
* * * *
5475625 ATAGTTTATACATATATAGTTTATATACATAGTTTAT
1 ATA-TATATATATATATAGTTTATAAACATAATTTAT
5475662 ATATATATATATATATAGTTCATATAAACATAATTTAT
1 ATATATATATATATATAGTT--TATAAACATAATTTAT
5475700 ATATATA
1 ATATATA
5475707 GCTTATAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
36 15 0.22
37 7 0.10
38 24 0.35
39 10 0.14
40 13 0.19
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (36 bp):
ATATATATATATATATAGTTTATAAACATAATTTAT
Found at i:5475724 original size:18 final size:19
Alignment explanation
Indices: 5475701--5475791 Score: 57
Period size: 18 Copynumber: 4.8 Consensus size: 19
5475691 ATAATTTATA
5475701 TATATAGCTTATA-ATAAT
1 TATATAGCTTATATATAAT
*
5475719 TATATAGTTTATATATAAAGT
1 TATATAGCTTATATAT-AA-T
**
5475740 TATATTATATTA-ATATAAAT
1 TATA-TAGCTTATATAT-AAT
*
5475760 TATATA-CTT-TA-ATACTT
1 TATATAGCTTATATATA-AT
*
5475777 TATATAGTTTATATA
1 TATATAGCTTATATA
5475792 CTCTTTACAC
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
16 1 0.02
17 9 0.16
18 17 0.29
19 6 0.10
20 8 0.14
21 12 0.21
22 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (19 bp):
TATATAGCTTATATATAAT
Found at i:5475740 original size:13 final size:13
Alignment explanation
Indices: 5475624--5475748 Score: 89
Period size: 13 Copynumber: 9.3 Consensus size: 13
5475614 ATATACTTTT
5475624 TATAGTTTATACATA
1 TATAGTTTAT--ATA
5475639 TATAGTTTATATA
1 TATAGTTTATATA
*
5475652 CATAGTTTATATA
1 TATAGTTTATATA
5475665 TATA---TATATA
1 TATAGTTTATATA
*
5475675 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
5475690 CATAATTTATATA
1 TATAGTTTATATA
5475703 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
5475721 TATAGTTTATATA
1 TATAGTTTATATA
*
5475734 TAAAG-TTATAT-
1 TATAGTTTATATA
5475745 TATA
1 TATA
5475749 TTAATATAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
10 10 0.11
11 3 0.03
12 6 0.07
13 32 0.36
14 3 0.03
15 23 0.26
16 3 0.03
17 3 0.03
18 7 0.08
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:5475773 original size:19 final size:18
Alignment explanation
Indices: 5475716--5475773 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 18
5475706 AGCTTATAAT
5475716 AATTATATAGTTTATATATA
1 AATTATATA-TTTA-ATATA
5475736 AAGTTATATTATATTAATATA
1 AA-TTATA-TAT-TTAATATA
5475757 AATTATATACTTTAATA
1 AATTATATA-TTTAATA
5475774 CTTTATATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.24
20 8 0.24
21 13 0.38
22 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (18 bp):
AATTATATATTTAATATA
Found at i:5475779 original size:17 final size:18
Alignment explanation
Indices: 5475759--5475793 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5475749 TTAATATAAA
5475759 TTATATACTTTA-ATACT
1 TTATATACTTTATATACT
*
5475776 TTATATAGTTTATATACT
1 TTATATACTTTATATACT
5475794 CTTTACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATATACTTTATATACT
Found at i:5475789 original size:9 final size:9
Alignment explanation
Indices: 5475759--5475793 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
5475749 TTAATATAAA
5475759 TTATATACT
1 TTATATACT
5475768 TTA-ATACT
1 TTATATACT
*
5475776 TTATATAGT
1 TTATATACT
5475785 TTATATACT
1 TTATATACT
5475794 CTTTACACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (9 bp):
TTATATACT
Found at i:5485195 original size:19 final size:21
Alignment explanation
Indices: 5485151--5485201 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
5485141 TACTGAAAAC
*
5485151 ATTATTATTTCTACCAGTTTT
1 ATTATTATTTGTACCAGTTTT
*
5485172 GTTATT-TTTGTACC-GTTTT
1 ATTATTATTTGTACCAGTTTT
*
5485191 ATTATTGTTTG
1 ATTATTATTTG
5485202 GTACTTTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.61
Consensus pattern (21 bp):
ATTATTATTTGTACCAGTTTT
Found at i:5485246 original size:21 final size:21
Alignment explanation
Indices: 5485222--5485266 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5485212 TGACATATTA
* * *
5485222 AAAAATATTGATATTTTAAGT
1 AAAAATAATAATATTCTAAGT
5485243 AAAAATAATAATATTCTAAGT
1 AAAAATAATAATATTCTAAGT
5485264 AAA
1 AAA
5485267 TTTTTACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAAATAATAATATTCTAAGT
Found at i:5486215 original size:70 final size:70
Alignment explanation
Indices: 5486084--5486220 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 70
5486074 TTCTCCAAAT
* *
5486084 ATTAAAAAACATAAAATTAACTGCAATCCACATAAATAAGTATTTTAACAAAAAGGTTTATCACA
1 ATTAAAAAACATAAAATTAACTGCAATCCACATAAATAAATATTTTAACAAAAACGTTTATCACA
5486149 TAAAC
66 TAAAC
* * *
5486154 ATTAAAACACATAACATTAACTGCAATCCATATAAATAAATAGTTTTAACAAAAACG-TTATCAC
1 ATTAAAAAACATAAAATTAACTGCAATCCACATAAATAAATA-TTTTAACAAAAACGTTTATCAC
5486218 ATA
65 ATA
5486221 TCAAGTTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 48 0.79
71 13 0.21
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28
Consensus pattern (70 bp):
ATTAAAAAACATAAAATTAACTGCAATCCACATAAATAAATATTTTAACAAAAACGTTTATCACA
TAAAC
Found at i:5488975 original size:48 final size:48
Alignment explanation
Indices: 5488912--5489024 Score: 172
Period size: 48 Copynumber: 2.4 Consensus size: 48
5488902 TTATCACTCG
* * **
5488912 TATCATCAGCCTCACCAACAGCAACCATTTCAGCAATACAATCACCCT
1 TATCATTACCCTCACCAACAAAAACCATTTCAGCAATACAATCACCCT
*
5488960 TATCATTACCCTCACCAACAAAAACCATTTCAGCAGTACAATCACCCT
1 TATCATTACCCTCACCAACAAAAACCATTTCAGCAATACAATCACCCT
*
5489008 TATCATTACCCTTACCA
1 TATCATTACCCTCACCA
5489025 GCATTTAGGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.35, C:0.36, G:0.04, T:0.24
Consensus pattern (48 bp):
TATCATTACCCTCACCAACAAAAACCATTTCAGCAATACAATCACCCT
Found at i:5489640 original size:12 final size:12
Alignment explanation
Indices: 5489619--5489650 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5489609 CCCAAATTCT
5489619 AAACCCAACATA
1 AAACCCAACATA
*
5489631 AAACCTAACATA
1 AAACCCAACATA
5489643 AAACCCAA
1 AAACCCAA
5489651 TATTTAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.09
Consensus pattern (12 bp):
AAACCCAACATA
Found at i:5493967 original size:647 final size:639
Alignment explanation
Indices: 5492727--5493969 Score: 2159
Period size: 647 Copynumber: 1.9 Consensus size: 639
5492717 AGAACACTTC
* * *
5492727 TCAAATAAAAAAGAAACATTGTGACTTTATCAATAAAAGAAAGTAATCTCATTATTTGTTTTTTC
1 TCAAATAAAAAAAAAACATTGTCACTTTATCAATAAAAGAAAGTAATCTCATTATTTGTTTTTTA
5492792 TTTAAAAAATAAAGTGATGAAATCTCAACAATTTTAATAAAGGAGTTTGGTAATTTCCTAAAAAT
66 TTTAAAAAATAAAGTGATGAAATCTCAACAATTTTAATAAAGGAGTTTGGTAATTTCCTAAAAAT
5492857 ATGAAACAAGTTAGAGATTTCTTGGACGAAATACCTAATCGTTGAGCTATAAATAATTCATTAAC
131 ATGAAACAAGTTAGAGATTTCTTGGACGAAATACCTAATCGTTGAGCTATAAATAATTCATTAAC
*
5492922 TTGACCAAATGAGAGCATTGTTTTGAGTGAGGTATACTTCAAAGAATTTCCAATACTATCGCTAT
196 TTGACCAAATGAGAGCATTGTTTTGAGAGAGGTATACTTCAAAGAATTTCCAATACTATCGCTAT
5492987 TTGCTGGCAAATAGAACATGAGTTTTTATTGATTCATTTGTGATATTATTTTAATTTTAACAAAT
261 TTGCTGGCAAATAGAACATGAGTTTTTATTGATTCATTTGTGATATTATTTTAATTTTAACAAAT
* * *
5493052 ATTAAATCTCAAGATATGATCTCACATATTTAGTTTTGAATTTATTAAATACTCATAACATATAT
326 ATTAAATCTCAAGATATGATCTCACATATTTAATTTTCAATTTACTAAATACTCATAACATATAT
* * *
5493117 ATAATCAAAATTTAATAATCATCATTTTTCAAAATGTACACTTCTATGAATTCAGATTTTAATCT
391 ATAATCAAAATGTAATAATCATCAATTTTCAAAATGTACACTTCTATGAATTCACATTTTAATCT
* *
5493182 TAATCTCATTTTACATGTATATGACATTTGAACCCAATAAGTGGTCTAAATGGTTAAAGAGAGTG
456 TAATCTCATTTAACAGGTATATGACATTTGAACCCAATAAGTGGTCTAAATGGTTAAAGAGAGTG
* * *
5493247 TTATTTTTTCTTGAAGTCCTAGGTTCGAGCAACTATGTCTGTAAGGTGTGTGTACGTCGTCAATA
521 CTATTTCTTCTTGAAGTCCTAGGTTCGAGCAACTATGTCTGTAAGGTATGTGTACGTCGTCAATA
5493312 ACTTAAAAGTATTATAAATAGAACACTTCTCAAATGTAAGTCGGATTCATAGAT
586 ACTTAAAAGTATTATAAATAGAACACTTCTCAAATGTAAGTCGGATTCATAGAT
*
5493366 TCAAATAAATAAAAAAACATTGTCACTTTGTCAATAAAAGAAAGTAATCTCATTATTTGTTTTTT
1 TCAAATAAA-AAAAAAACATTGTCACTTTATCAATAAAAGAAAGTAATCTCATTATTTGTTTTTT
5493431 ATTTAAAAAATAAAGTGATGAAATCTCAACAATTTTAATAAAGGAGTTTGGTAATTTCCTAAAAA
65 ATTTAAAAAATAAAGTGATGAAATCTCAACAATTTTAATAAAGGAGTTTGGTAATTTCCTAAAAA
*
5493496 TATGAAACAAGTTAGAGATTTCTTGGACGAAATACCTAATCTTTGAGCTATAAATAATTCATTAA
130 TATGAAACAAGTTAGAGATTTCTTGGACGAAATACCTAATCGTTGAGCTATAAATAATTCATTAA
* *
5493561 CTTGACCAAATGAGAGCATTGTTTTGAGAGAGTTAT-CTTCAAAGAA-TTCCAATACTATTGCTA
195 CTTGACCAAATGAGAGCATTGTTTTGAGAGAGGTATACTTCAAAGAATTTCCAATACTATCGCTA
5493624 TTTGCTGGCAAATAGAACTATGGAAGCATGAGTTTTTATTGATTCATTTGTGATATTATTTTAAT
260 TTTGCTGGC----A-AA-TA--GAA-CATGAGTTTTTATTGATTCATTTGTGATATTATTTTAAT
*
5493689 TTTAACAAATATTAAATCTCAAGATATGATCTCAGATATTTAATTTTCAATTTACTAAATACTCA
316 TTTAACAAATATTAAATCTCAAGATATGATCTCACATATTTAATTTTCAATTTACTAAATACTCA
*
5493754 TAACATATATATAATCAAAATGTAATTATCATCAATTTTCAAAATGTACACTTCTATGAATTCAC
381 TAACATATATATAATCAAAATGTAATAATCATCAATTTTCAAAATGTACACTTCTATGAATTCAC
* *
5493819 ATTTTAATCTTAATCTCATTTAACAGGTATATGGCATTTGAACCTAATAAGTGGTCTAAATGGTT
446 ATTTTAATCTTAATCTCATTTAACAGGTATATGACATTTGAACCCAATAAGTGGTCTAAATGGTT
5493884 AAAGAGAGTGCTA-TTCTTCATTGAAGTCCTAGGTTCGAGCAACTATGTCTGTAAGGTATGTGTA
511 AAAGAGAGTGCTATTTCTTC-TTGAAGTCCTAGGTTCGAGCAACTATGTCTGTAAGGTATGTGTA
5493948 CGTCGTCAATAACTTAAAAGTA
575 CGTCGTCAATAACTTAAAAGTA
5493970 ATCTCATTAT
Statistics
Matches: 570, Mismatches: 23, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
638 25 0.04
639 19 0.03
640 214 0.38
642 1 0.00
643 2 0.00
644 2 0.00
646 8 0.01
647 299 0.52
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (639 bp):
TCAAATAAAAAAAAAACATTGTCACTTTATCAATAAAAGAAAGTAATCTCATTATTTGTTTTTTA
TTTAAAAAATAAAGTGATGAAATCTCAACAATTTTAATAAAGGAGTTTGGTAATTTCCTAAAAAT
ATGAAACAAGTTAGAGATTTCTTGGACGAAATACCTAATCGTTGAGCTATAAATAATTCATTAAC
TTGACCAAATGAGAGCATTGTTTTGAGAGAGGTATACTTCAAAGAATTTCCAATACTATCGCTAT
TTGCTGGCAAATAGAACATGAGTTTTTATTGATTCATTTGTGATATTATTTTAATTTTAACAAAT
ATTAAATCTCAAGATATGATCTCACATATTTAATTTTCAATTTACTAAATACTCATAACATATAT
ATAATCAAAATGTAATAATCATCAATTTTCAAAATGTACACTTCTATGAATTCACATTTTAATCT
TAATCTCATTTAACAGGTATATGACATTTGAACCCAATAAGTGGTCTAAATGGTTAAAGAGAGTG
CTATTTCTTCTTGAAGTCCTAGGTTCGAGCAACTATGTCTGTAAGGTATGTGTACGTCGTCAATA
ACTTAAAAGTATTATAAATAGAACACTTCTCAAATGTAAGTCGGATTCATAGAT
Found at i:5498803 original size:17 final size:16
Alignment explanation
Indices: 5498781--5498841 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
5498771 TTCAGAAAAT
*
5498781 AAAAATAAAAAATATGA
1 AAAAATAAAAAA-GTGA
**
5498798 AAAAATGTTAAAAGTGA
1 AAAAAT-AAAAAAGTGA
5498815 AAAAA-AAAAGAAGTGA
1 AAAAATAAAA-AAGTGA
5498831 AAAAATAAAAA
1 AAAAATAAAAA
5498842 TAAAACAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 2 0.06
16 12 0.33
17 18 0.50
18 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (16 bp):
AAAAATAAAAAAGTGA
Found at i:5498828 original size:16 final size:17
Alignment explanation
Indices: 5498809--5498840 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5498799 AAAATGTTAA
5498809 AAGTGAAAAAA-AAAAG
1 AAGTGAAAAAATAAAAG
5498825 AAGTGAAAAAATAAAA
1 AAGTGAAAAAATAAAA
5498841 ATAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAGTGAAAAAATAAAAG
Found at i:5498862 original size:16 final size:16
Alignment explanation
Indices: 5498832--5498861 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5498822 AAGAAGTGAA
5498832 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
5498848 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
5498862 AAGTGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:5502117 original size:27 final size:27
Alignment explanation
Indices: 5502087--5502142 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5502077 GAGTGTTACC
5502087 AAGAGAAAACATAAATACTTCACCTGA
1 AAGAGAAAACATAAATACTTCACCTGA
5502114 AAGAGAAAACATAAATACTTCACCTGA
1 AAGAGAAAACATAAATACTTCACCTGA
5502141 AA
1 AA
5502143 TTTACTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (27 bp):
AAGAGAAAACATAAATACTTCACCTGA
Found at i:5502700 original size:9 final size:10
Alignment explanation
Indices: 5502677--5502704 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5502667 AAGGAGGTTA
5502677 AAAAAATGCT
1 AAAAAATGCT
5502687 AAAAAATGCT
1 AAAAAATGCT
5502697 AAAAAATG
1 AAAAAATG
5502705 GTGTGTCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.11, T:0.18
Consensus pattern (10 bp):
AAAAAATGCT
Found at i:5503056 original size:118 final size:117
Alignment explanation
Indices: 5502848--5503108 Score: 407
Period size: 118 Copynumber: 2.2 Consensus size: 117
5502838 AAAAAATATA
* * * *
5502848 GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGTT
1 GACGATAACATAATCGGTTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
* *
5502913 TATATAACGTAATAGGTAGCGCCTTTTTAAAGCTGAT-GGGACTTTGGAAATCC
66 TATATAAAGTAATAGGTAGCGCCTTTTT-AAGCTAATAGGG-CTTTGGAAATCC
* *
5502966 GACGATAACATAATCGGTTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGTGCT
1 GACGATAACATAATCGGTTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
*
5503031 TATATAAAGTAATAGGTAGCGCCTTTTTAATCTAATAGGGCTTTGGAAATCC
66 TATATAAAGTAATAGGTAGCGCCTTTTTAAGCTAATAGGGCTTTGGAAATCC
*
5503083 GACGATAACATAATCAGTTAATTACT
1 GACGATAACATAATCGGTTAATTACT
5503109 TATATTGTTA
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
117 43 0.33
118 89 0.67
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (117 bp):
GACGATAACATAATCGGTTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
TATATAAAGTAATAGGTAGCGCCTTTTTAAGCTAATAGGGCTTTGGAAATCC
Found at i:5503404 original size:118 final size:118
Alignment explanation
Indices: 5503180--5503436 Score: 340
Period size: 118 Copynumber: 2.2 Consensus size: 118
5503170 CTGATAGAGC
* *
5503180 CTTAGAAATCCGACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATAT
1 CTTAGAAATCCGACGATAACATAACCGATTAATTACCGAAAACATTATCAAGCATAATAACATAT
* * * * *
5503245 TAGGTAACGCTTATATAACATAATATGTAGCGTCTTTTTAAAG-CGTTTGGGG-
66 TAGGTAACGCTTATATAACATAATAGGTAGCGACTTATTAAAGATG-ATGGGGT
* * *
5503297 CTTTGGAAATCCGACGATAACATAACTGGTTAATTACCGAAAACATTATCAAGCATAATAACATA
1 C-TTAGAAATCCGACGATAACATAACCGATTAATTACCGAAAACATTATCAAGCATAATAACATA
* * * *
5503362 TTAGGTAGCGCTTATGTAACGTAATAGGTTGC-ACATTATTAAAGATGATGGGGT
65 TTAGGTAACGCTTATATAACATAATAGGTAGCGAC-TTATTAAAGATGATGGGGT
5503416 CTTAGAAATCCGACGATAACA
1 CTTAGAAATCCGACGATAACA
5503437 AAATAGGTTA
Statistics
Matches: 121, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
117 2 0.02
118 117 0.97
119 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (118 bp):
CTTAGAAATCCGACGATAACATAACCGATTAATTACCGAAAACATTATCAAGCATAATAACATAT
TAGGTAACGCTTATATAACATAATAGGTAGCGACTTATTAAAGATGATGGGGT
Found at i:5506481 original size:21 final size:21
Alignment explanation
Indices: 5506431--5506481 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
5506421 TACATATACC
*
5506431 AAAAGTATCGATACTTTCTAT
1 AAAAGTATTGATACTTTCTAT
5506452 AAAAGTATTGATACTTTCTAT
1 AAAAGTATTGATACTTTCTAT
*
5506473 AAAATTATT
1 AAAAGTATT
5506482 TTACCATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (21 bp):
AAAAGTATTGATACTTTCTAT
Found at i:5509524 original size:24 final size:23
Alignment explanation
Indices: 5509497--5509573 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
5509487 CACCACAACT
*
5509497 TGTATAAAATGCTCTGAAGTGCCA
1 TGTA-AAAATGCTCCGAAGTGCCA
*
5509521 TGTAGAAATGCTCCGAAGTGCCA
1 TGTAAAAATGCTCCGAAGTGCCA
* * * *
5509544 CGTAGAAATGCACCGAAGTGCTA
1 TGTAAAAATGCTCCGAAGTGCCA
*
5509567 TATAAAA
1 TGTAAAA
5509574 TATCCCGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (23 bp):
TGTAAAAATGCTCCGAAGTGCCA
Found at i:5509529 original size:23 final size:23
Alignment explanation
Indices: 5509503--5509564 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
5509493 AACTTGTATA
* *
5509503 AAATGCTCTGAAGTGCCATGTAG
1 AAATGCTCCGAAGTGCCACGTAG
5509526 AAATGCTCCGAAGTGCCACGTAG
1 AAATGCTCCGAAGTGCCACGTAG
*
5509549 AAATGCACCGAAGTGC
1 AAATGCTCCGAAGTGC
5509565 TATATAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
AAATGCTCCGAAGTGCCACGTAG
Found at i:5509637 original size:21 final size:21
Alignment explanation
Indices: 5509613--5509671 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
5509603 TAGGGACTAT
5509613 ATATATATTCCAAAGGACCAA
1 ATATATATTCCAAAGGACCAA
* * **
5509634 ATATGTA-TCTCAAAGAACCGC
1 ATATATATTC-CAAAGGACCAA
*
5509655 ATATATGTTCCAAAGGA
1 ATATATATTCCAAAGGA
5509672 TTATATATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (21 bp):
ATATATATTCCAAAGGACCAA
Found at i:5516575 original size:23 final size:23
Alignment explanation
Indices: 5516549--5516612 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
5516539 AGCTCGTATA
5516549 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* ** *
5516572 AAATGCACCGATGTATCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
5516595 AAATGCACCAAAGTGCCA
1 AAATGCACCGAAGTGCCA
5516613 TATAAAATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:5520717 original size:200 final size:197
Alignment explanation
Indices: 5520374--5520863 Score: 658
Period size: 200 Copynumber: 2.4 Consensus size: 197
5520364 TATCGATGTT
5520374 TTCATACTGGACAAAATGTATCGATACAAGTTTAAAAAGTATCGATACTTTTTGTTTACCTATTC
1 TTCATACTGGACAAAA-GTATCGATACAA-TTTAAAAAGTATCGATACTTTTTG-TTACCTATTC
** * * ** *
5520439 TCTCATTAAA-CCGATATATTTTTACCCATTACATTGTATATTTACCTATTACTTTATAATTATC
63 TCTCATTAAATTAG-TATATTTTTACCCATTACATTGTAAAATTACCTATTACACTATAATAATC
*
5520503 GGTTTCGATGTTTTAAGGATCGATACTTATGATACATGTATCGATACTTTATGCATCCATCTCGT
127 GGTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATCCATCTCGT
*
5520568 TTGGGA
192 TTAGGA
* * *
5520574 TTCATACTGGACTAAAAGTATTGATACTATTTAAATAAGTATCGATACTTTATGTATACCTATTC
1 TTCATACTGGAC-AAAAGTATCGATACAATTTAAA-AAGTATCGATACTTTTTGT-TACCTATTC
** *
5520639 TCTCATTAAATTAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACACTATAATAATTG
63 TCTCATTAAATTAGTATATTTTTACCCATTACATTGTAAAATTACCTATTACACTATAATAATCG
* * *
5520704 GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATGGATACTTTATGCGTGCATCTCGTT
128 GTTTCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATCCATCTCGTT
5520769 TAGGA
193 TAGGA
* * * *
5520774 TTCATACTGGACAAAAAATATCGATACAACTTAAAAAACTATCGATACTTTTTGGTTACATATTC
1 TTCATACTGGAC-AAAAGTATCGATACAA-TTTAAAAAGTATCGATACTTTTT-GTTACCTATTC
* *
5520839 TTTCATTAAATTGGTATATGTTTTA
63 TCTCATTAAATTAGTATAT-TTTTA
5520864 AGGATCGATA
Statistics
Matches: 255, Mismatches: 28, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
199 7 0.03
200 231 0.91
201 17 0.07
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (197 bp):
TTCATACTGGACAAAAGTATCGATACAATTTAAAAAGTATCGATACTTTTTGTTACCTATTCTCT
CATTAAATTAGTATATTTTTACCCATTACATTGTAAAATTACCTATTACACTATAATAATCGGTT
TCGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATCCATCTCGTTTAG
GA
Found at i:5520984 original size:146 final size:146
Alignment explanation
Indices: 5520710--5520994 Score: 428
Period size: 146 Copynumber: 2.0 Consensus size: 146
5520700 ATTGGTTTCG
* * * * *
5520710 ATGTTTTAAGGATCGATACTTATCATACATGTATGGATACTTTATGCGTGCATCTCGTTTAGGAT
1 ATGTTTTAAGGATCGATACGTATCAAACATGTATCGATACATTATGCGTCCATCTCGTTTAGGAT
*
5520775 TCATACTGGACAAAAAATATCGATACAACTTAAAAAACTATCGATACTTTTTGGTTACATATTCT
66 TCATACTGGACAAAAAATATCGATACAACTGAAAAAACTATCGATACTTTTTGGTTACATATTCT
*
5520840 TTCATTAAATTGGTAT
131 CTCATTAAATTGGTAT
* * *
5520856 ATGTTTTAAGGATCGATACGTCTTAAACATGTATCGATACATTATGCGTCCATCTCGTTTGGGAT
1 ATGTTTTAAGGATCGATACGTATCAAACATGTATCGATACATTATGCGTCCATCTCGTTTAGGAT
* * * *
5520921 TCATACTGGA-AAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTC
66 TCATACTGGACAAAAA-ATATCGATACAACTGAAAAAACTATCGATACTTTTTGGTTACATATTC
5520985 TCTCATTAAA
130 TCTCATTAAA
5520995 CCAATATATA
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
145 5 0.04
146 119 0.96
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (146 bp):
ATGTTTTAAGGATCGATACGTATCAAACATGTATCGATACATTATGCGTCCATCTCGTTTAGGAT
TCATACTGGACAAAAAATATCGATACAACTGAAAAAACTATCGATACTTTTTGGTTACATATTCT
CTCATTAAATTGGTAT
Found at i:5521324 original size:146 final size:146
Alignment explanation
Indices: 5521060--5521340 Score: 431
Period size: 146 Copynumber: 1.9 Consensus size: 146
5521050 GTTTTGATGT
* * * *
5521060 TTTAAGGATCGATACTCATCATACATGTATCGATACTTTATGCATGCATCTCGTTTGGTATTCAT
1 TTTAAGGATCGATACTCATCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
* *
5521125 ACTGGACAAAAATTATCAATACAACTTAAAAAACTATCGATACTTTTTATTTACATATTCTCTCA
66 ACTAGACAAAAATTATCAATACAACTGAAAAAACTATCGATACTTTTTATTTACATATTCTCTCA
5521190 TTAAACCGGTATATGC
131 TTAAACCGGTATATGC
5521206 TTTAAGGATCGATACGTC-TCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCA
1 TTTAAGGATCGATAC-TCATCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCA
* * * * *
5521270 TACTAGA-AAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTTT
65 TACTAGACAAAAAT-TATCAATACAACTGAAAAAACTATCGATACTTTTTATTTACATATTCTCT
5521334 CATTAAA
129 CATTAAA
5521341 TAGGTAACAA
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
145 6 0.05
146 114 0.93
147 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (146 bp):
TTTAAGGATCGATACTCATCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
ACTAGACAAAAATTATCAATACAACTGAAAAAACTATCGATACTTTTTATTTACATATTCTCTCA
TTAAACCGGTATATGC
Found at i:5521444 original size:346 final size:346
Alignment explanation
Indices: 5520514--5521411 Score: 1306
Period size: 346 Copynumber: 2.6 Consensus size: 346
5520504 GTTTCGATGT
* * * * *
5520514 TTTAAGGATCGATACTTATGATACATGTATCGATACTTTATGCATCCATCTCGTTTGGGATTCAT
1 TTTAAGGATCGATACGTCTCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
* * * * * * * *
5520579 ACTGGACTAAAA-GTATTGATACTATTTAAATAAGTATCGATACTTTATGTATACCTATTCTCTC
66 ACTGGA-AAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTCTC
* * *
5520643 ATTAAATTAGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACAC-TATAATAATTGGTT
130 ATTAAACTAGTATATATTTACCGGTTACATTGTAAATTTACCTATTAC-CTTATAATAATTGGTT
* * *
5520707 TCGATGTTTTAAGGATCGATACTTATCATACATGTATGGATACTTTATGCGTGCATCTCGTTTAG
194 TTGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATGCATCTCGTTTAG
* *
5520772 GATTCATACTGGACAAAAAATATCGATACAACTTAAAAAACTATCGATACTTTTTGGTTACATAT
259 GATTCATACTGGACAAAAAATATCAATACAACTTAAAAAACTATCGATACTTTTTAGTTACATAT
* ** *
5520837 TCTTTCATTAAATTGGTATATGT
324 TCTCTCATTAAACCGGTATATGC
* *
5520860 TTTAAGGATCGATACGTCTTAAACATGTATCGATACATTATGCGTCCATCTCGTTTGGGATTCAT
1 TTTAAGGATCGATACGTCTCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
5520925 ACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTCTCA
66 ACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTCTCA
* * * * * * *
5520990 TTAAACCAATATATATTTACTGGTTACATTGTATATTTACCTATTACTTTATAATTATAGGTTTT
131 TTAAACTAGTATATATTTACCGGTTACATTGTAAATTTACCTATTACCTTATAATAATTGGTTTT
*
5521055 GATGTTTTAAGGATCGATACTCATCATACATGTATCGATACTTTATGCATGCATCTCGTTT-GGT
196 GATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATGCATCTCGTTTAGG-
* *
5521119 ATTCATACTGGACAAAAATTATCAATACAACTTAAAAAACTATCGATACTTTTTATTTACATATT
260 ATTCATACTGGACAAAAAATATCAATACAACTTAAAAAACTATCGATACTTTTTAGTTACATATT
5521184 CTCTCATTAAACCGGTATATGC
325 CTCTCATTAAACCGGTATATGC
5521206 TTTAAGGATCGATACGTCTCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
1 TTTAAGGATCGATACGTCTCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
* *
5521271 ACTAGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTTTCA
66 ACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTCTCA
* * *
5521336 TTAAA-TAGGTA-ACAATATACCGCTTACATTGTAAATTTA-CTGATTACCTTCA-AATAATTGG
131 TTAAACTA-GTATA-TATTTACCGGTTACATTGTAAATTTACCT-ATTACCTT-ATAATAATTGG
5521397 TTTTGATGTTTTAAG
192 TTTTGATGTTTTAAG
5521412 AATCTATGCT
Statistics
Matches: 495, Mismatches: 50, Indels: 14
0.89 0.09 0.03
Matches are distributed among these distances:
345 10 0.02
346 484 0.98
347 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (346 bp):
TTTAAGGATCGATACGTCTCAAACATGTATCGATACATTATGCATCCATCTCGTTTGGGATTCAT
ACTGGAAAAAATGTATCGATACAACTGAAAAAAGTATCGATACTTTTTGTTTACCTATTCTCTCA
TTAAACTAGTATATATTTACCGGTTACATTGTAAATTTACCTATTACCTTATAATAATTGGTTTT
GATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATGCATCTCGTTTAGGA
TTCATACTGGACAAAAAATATCAATACAACTTAAAAAACTATCGATACTTTTTAGTTACATATTC
TCTCATTAAACCGGTATATGC
Found at i:5523423 original size:66 final size:66
Alignment explanation
Indices: 5523347--5523472 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
5523337 TCATCATCCC
*
5523347 CTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCTATCAAATTTTCCACCCATCACCA
1 CTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAAATTTTCCACCCATCACCA
5523412 T
66 T
* * * *
5523413 CTTAAGTTCACCCCTCAATTCCACAACTTCTTTTACCACTCCATCTATTTTTCCACCCAT
1 CTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAAATTTTCCACCCAT
5523473 TTCCCCCTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.25, C:0.40, G:0.02, T:0.33
Consensus pattern (66 bp):
CTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAAATTTTCCACCCATCACCA
T
Found at i:5523483 original size:66 final size:66
Alignment explanation
Indices: 5523338--5523484 Score: 204
Period size: 66 Copynumber: 2.2 Consensus size: 66
5523328 CAACCACTCT
* *
5523338 CATCATCCCCTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCTATCAAATTTTCCAC
1 CATCACCCCCTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAAATTTTCCAC
5523403 C
66 C
** * * * *
5523404 CATCACCATCTTAAGTTCACCCCTCAATTCCACAACTTCTTTTACCACTCCATCTATTTTTCCAC
1 CATCACCCCCTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAAATTTTCCAC
5523469 C
66 C
**
5523470 CATTTCCCCCTTAAG
1 CATCACCCCCTTAAG
5523485 CCTCTGAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.24, C:0.41, G:0.02, T:0.33
Consensus pattern (66 bp):
CATCACCCCCTTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAAATTTTCCAC
C
Found at i:5526136 original size:183 final size:183
Alignment explanation
Indices: 5525828--5526185 Score: 619
Period size: 183 Copynumber: 2.0 Consensus size: 183
5525818 GCGCTTTACT
*
5525828 AGTTTTTTCATATTTTGACCTGTTATATTGTTATGTATCAATACATGTTTATAAAATATTGATAC
1 AGTTTTTTCATATTTTGACCTGTTATATTGTTATGTATCAATACATGTTTATAAAATATCGATAC
*
5525893 TTTATAGGCGCTATTATTGTTTTCCTTTTAAATTCCAAAAGTATCAAAACTTATTTGAATGGTAT
66 TTTATAGGCGCTAGTATTGTTTTCCTTTTAAATTCCAAAAGTATCAAAACTTATTTGAATGGTAT
*
5525958 CGATACCTTCAACATATCCGGTATCTCTTTACCGGTTTTGTCATAATGAAACC
131 CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACC
* * *
5526011 AGTTTTTTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
1 AGTTTTTTCATATTTTGACCTGTTATATTGTTATGTATCAATACATGTTTATAAAATATCGATAC
* * *
5526076 TTTATAGGCGCTAGTATTGCTTTT-CTTTTTAATTCCAAAAGTATCGATACTTATTTGAATGGTA
66 TTTATAGGCGCTAGTATTG-TTTTCCTTTTAAATTCCAAAAGTATCAAAACTTATTTGAATGGTA
5526140 TCGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATA
130 TCGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATA
5526186 TTTTTACCTG
Statistics
Matches: 165, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 161 0.98
184 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (183 bp):
AGTTTTTTCATATTTTGACCTGTTATATTGTTATGTATCAATACATGTTTATAAAATATCGATAC
TTTATAGGCGCTAGTATTGTTTTCCTTTTAAATTCCAAAAGTATCAAAACTTATTTGAATGGTAT
CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACC
Found at i:5526288 original size:163 final size:163
Alignment explanation
Indices: 5526012--5526350 Score: 590
Period size: 163 Copynumber: 2.1 Consensus size: 163
5526002 AATGAAACCA
*
5526012 GTTTTTTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACT
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACT
*
5526077 TTATAGGCGCTAGTATTGCTTTTCTTTTTAATTCCAAAAGTATCGATACTTATTTGAATGGTATC
66 TTATAGGCGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATC
*
5526142 GATACCTTCAACATATCCGGTAGCTCTTTACCG
131 GATACCTTCAACATATCCGGTAGCACTTTACCG
*
5526175 GTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATTGATACT
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACT
* *
5526240 TTATAGGCGCTATTACTT-CTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTTAATGGTAT
66 TTATAGGCGCTAGTA-TTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTAT
*
5526304 CGATACCTTCAACATATCCGGTAGCACTTTATCG
130 CGATACCTTCAACATATCCGGTAGCACTTTACCG
*
5526338 ATTTTGTCATATT
1 GTTTTGTCATATT
5526351 GAACTCGGGT
Statistics
Matches: 167, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
163 165 0.99
164 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (163 bp):
GTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACT
TTATAGGCGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATC
GATACCTTCAACATATCCGGTAGCACTTTACCG
Found at i:5535887 original size:15 final size:15
Alignment explanation
Indices: 5535867--5535897 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5535857 ATTTAAGCAC
5535867 ATAAATAAAAATAAA
1 ATAAATAAAAATAAA
*
5535882 ATAAATAACAATAAA
1 ATAAATAAAAATAAA
5535897 A
1 A
5535898 ACGTTCTTTG
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:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAATAAAAATAAA
Found at i:5537299 original size:11 final size:11
Alignment explanation
Indices: 5537269--5537302 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5537259 CATTAAGCAC
5537269 CATAAGAAAAA
1 CATAAGAAAAA
*
5537280 CA-AATAAAAA
1 CATAAGAAAAA
5537290 CATAAGAAAAA
1 CATAAGAAAAA
5537301 CA
1 CA
5537303 ATCATCCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.74, C:0.12, G:0.06, T:0.09
Consensus pattern (11 bp):
CATAAGAAAAA
Found at i:5538227 original size:16 final size:16
Alignment explanation
Indices: 5538204--5538243 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
5538194 ACAATTAATA
5538204 TATATTTAAAATATTAT
1 TATATTTAAAATA-TAT
*
5538221 T-TATTTAAAGTATAT
1 TATATTTAAAATATAT
5538236 TATATTTA
1 TATATTTA
5538244 GTAAGCGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTTAAAATATAT
Found at i:5538330 original size:2 final size:2
Alignment explanation
Indices: 5538323--5538391 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
5538313 CAATTGTATG
5538323 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
5538365 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
5538392 TTTATTGTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5540675 original size:19 final size:19
Alignment explanation
Indices: 5540639--5540677 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5540629 GGTCCAAAAA
* *
5540639 CGGTCTGAACCTGTTTGAC
1 CGGTCTGAACCGGGTTGAC
*
5540658 CGGTCTGAATCGGGTTGAC
1 CGGTCTGAACCGGGTTGAC
5540677 C
1 C
5540678 AGTCGGACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (19 bp):
CGGTCTGAACCGGGTTGAC
Found at i:5540763 original size:29 final size:28
Alignment explanation
Indices: 5540721--5540918 Score: 189
Period size: 29 Copynumber: 6.9 Consensus size: 28
5540711 ATCCGGTGAC
*
5540721 ATTCTGGGAAATATTTTGGAATAAATGAT
1 ATTCTGGGAAATATTTT-GAAAAAATGAT
** *
5540750 ATTCTGGGAAATATTTTGAAATAGGTGAC
1 ATTCTGGGAAATATTTTGAAA-AAATGAT
** *
5540779 ATTCAAGGAAATATTTTGAAAAAAGGTGAC
1 ATTCTGGGAAATATTTTGAAAAAA--TGAT
*
5540809 ATTTTGGGAAATATTTTGAAAAAAGTGAT
1 ATTCTGGGAAATATTTTGAAAAAA-TGAT
**
5540838 ATTCTATGAAATATTTTGAAAAAATGAT
1 ATTCTGGGAAATATTTTGAAAAAATGAT
* * * * *
5540866 ATTATGGGAATTATTTTGAAAAAGGTTAC
1 ATTCTGGGAAATATTTTGAAAAA-ATGAT
* *
5540895 ATTCTAGGAATTATTTTGAAAAAA
1 ATTCTGGGAAATATTTTGAAAAAA
5540919 AGTGACATTT
Statistics
Matches: 140, Mismatches: 25, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
28 27 0.19
29 88 0.63
30 25 0.18
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (28 bp):
ATTCTGGGAAATATTTTGAAAAAATGAT
Found at i:5540849 original size:59 final size:57
Alignment explanation
Indices: 5540715--5540934 Score: 269
Period size: 59 Copynumber: 3.8 Consensus size: 57
5540705 GACCCAATCC
* * * * *
5540715 GGTGACATTCTGGGAAATATTTTGGAATAAATGATATTCTGGGAAATATTTTGAAATA
1 GGTGACATTCTAGGAAATATTTT-GAAAAAATGACATTTTGGGAAATATTTTGAAAAA
*
5540773 GGTGACATTCAAGGAAATATTTTGAAAAAAGGTGACATTTTGGGAAATATTTTGAAAAA
1 GGTGACATTCTAGGAAATATTTTGAAAAAA--TGACATTTTGGGAAATATTTTGAAAAA
* * * * * *
5540832 AGTGATATTCTATGAAATATTTTGAAAAAATGATATTATGGGAATTATTTTGAAAAA
1 GGTGACATTCTAGGAAATATTTTGAAAAAATGACATTTTGGGAAATATTTTGAAAAA
* *
5540889 GGTTACATTCTAGGAATTATTTTGAAAAAAAGTGACATTTTGGGAA
1 GGTGACATTCTAGGAAATATTTTG-AAAAAA-TGACATTTTGGGAA
5540935 TTTTCAAATT
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
57 49 0.36
58 27 0.20
59 62 0.45
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (57 bp):
GGTGACATTCTAGGAAATATTTTGAAAAAATGACATTTTGGGAAATATTTTGAAAAA
Found at i:5543014 original size:17 final size:17
Alignment explanation
Indices: 5542992--5543033 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
5542982 GTTTGACCCG
5542992 ACCCGACCTGTTGACCA
1 ACCCGACCTGTTGACCA
*
5543009 ACCCGACCTGTTGACCG
1 ACCCGACCTGTTGACCA
5543026 ACCCGACC
1 ACCCGACC
5543034 CGACCCGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.45, G:0.19, T:0.14
Consensus pattern (17 bp):
ACCCGACCTGTTGACCA
Found at i:5543015 original size:22 final size:22
Alignment explanation
Indices: 5542986--5543055 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
5542976 GAACCGGTTT
5542986 GACCCGACCCGACCTGTTGACC
1 GACCCGACCCGACCTGTTGACC
5543008 -A----ACCCGACCTGTTGACC
1 GACCCGACCCGACCTGTTGACC
* *
5543025 GACCCGACCCGACCCGTTGACT
1 GACCCGACCCGACCTGTTGACC
5543047 GACCCGACC
1 GACCCGACC
5543056 TGATGACATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 16 0.39
18 1 0.02
21 1 0.02
22 23 0.56
ACGTcount: A:0.20, C:0.46, G:0.21, T:0.13
Consensus pattern (22 bp):
GACCCGACCCGACCTGTTGACC
Found at i:5543034 original size:39 final size:39
Alignment explanation
Indices: 5542986--5543062 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
5542976 GAACCGGTTT
* *
5542986 GACCCGACCCGACCTGTTGACCAACCCGACCTGTTGACC
1 GACCCGACCCGACCCGTTGACCAACCCGACCTGATGACC
**
5543025 GACCCGACCCGACCCGTTGACTGACCCGACCTGATGAC
1 GACCCGACCCGACCCGTTGACCAACCCGACCTGATGAC
5543063 ATTCTAGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.21, C:0.43, G:0.22, T:0.14
Consensus pattern (39 bp):
GACCCGACCCGACCCGTTGACCAACCCGACCTGATGACC
Found at i:5543103 original size:29 final size:29
Alignment explanation
Indices: 5543059--5543267 Score: 276
Period size: 29 Copynumber: 7.2 Consensus size: 29
5543049 CCCGACCTGA
* *
5543059 TGACATTCTAGGAAATATTTTGAAATAGG
1 TGACATTCTGGGAAATATTTTGAAAAAGG
* * *
5543088 TAACATTTTGGGAAATATTTTGAAAAAAG
1 TGACATTCTGGGAAATATTTTGAAAAAGG
*
5543117 TGGCATTCTGGGAAATATTTTGAAAAAGG
1 TGACATTCTGGGAAATATTTTGAAAAAGG
* *
5543146 TGACATTCGGGGAAATATTTTGATAAAGG
1 TGACATTCTGGGAAATATTTTGAAAAAGG
5543175 TGACATTCTGGGAAATATTTTGAAAAAGG
1 TGACATTCTGGGAAATATTTTGAAAAAGG
* * * *
5543204 TGATATTATAGGAATTATTTTGAAAAAGG
1 TGACATTCTGGGAAATATTTTGAAAAAGG
** *
5543233 TGACATTCTAAGAATTATTTTGAAAAA-G
1 TGACATTCTGGGAAATATTTTGAAAAAGG
5543261 TGACATT
1 TGACATT
5543268 TTGAGAATTT
Statistics
Matches: 159, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
28 8 0.05
29 151 0.95
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.34
Consensus pattern (29 bp):
TGACATTCTGGGAAATATTTTGAAAAAGG
Found at i:5544231 original size:63 final size:63
Alignment explanation
Indices: 5544163--5544286 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
5544153 CTAATGTGAC
* * * *
5544163 TCTTAGGTAGGCTCTACGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
5544226 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
5544287 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.02
63 51 0.96
64 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:5544237 original size:32 final size:31
Alignment explanation
Indices: 5544163--5544247 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
5544153 CTAATGTGAC
* *
5544163 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
5544194 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
*
5544226 TCTTAGGTAGGCCCCACGGCCC
1 TCTTAGGTAGGCCCTACGGCCC
5544248 CGAAATCTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.55
32 19 0.45
ACGTcount: A:0.15, C:0.31, G:0.29, T:0.25
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:5549239 original size:23 final size:23
Alignment explanation
Indices: 5549194--5549239 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5549184 TAAAATAAAT
* * * *
5549194 GAAAAATATTAAATTTTGGAAAA
1 GAAAAATAATAAAATATGAAAAA
5549217 GAAAAATAATAAAATATGAAAAA
1 GAAAAATAATAAAATATGAAAAA
5549240 ATGTTAAAAG
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:0.00, G:0.11, T:0.24
Consensus pattern (23 bp):
GAAAAATAATAAAATATGAAAAA
Found at i:5549282 original size:41 final size:44
Alignment explanation
Indices: 5549235--5549336 Score: 102
Period size: 46 Copynumber: 2.3 Consensus size: 44
5549225 ATAAAATATG
*
5549235 AAAAAATGTTAAAAG-A-GAAAATAAAAATAAAACAAAA-CAAA
1 AAAAAATGTTAAAAGAAGGAAAATAAAAATAAAACAAAATAAAA
* ***
5549276 ATAAAATAAAAAAAGAAGTGGGAAAATAAAAATAAAACAAAATAAAA
1 AAAAAATGTTAAAAGAA---GGAAAATAAAAATAAAACAAAATAAAA
5549323 AAAGAAATGTTAAA
1 AAA-AAATGTTAAA
5549337 TTTTAAAGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
41 11 0.24
42 1 0.02
46 21 0.47
47 5 0.11
48 7 0.16
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.14
Consensus pattern (44 bp):
AAAAAATGTTAAAAGAAGGAAAATAAAAATAAAACAAAATAAAA
Found at i:5558133 original size:225 final size:226
Alignment explanation
Indices: 5557837--5558438 Score: 836
Period size: 226 Copynumber: 2.7 Consensus size: 226
5557827 AGCTAATGGG
* * * * * *
5557837 GCTTTAGAAATCCAACGACAACATAATCGGTTAATTACTGGAAATATTATCGAGCATAATAACTT
1 GCTTTAGAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACAT
*
5557902 ATTAGGTAGCACTTATATAACGTAATAGGTAGCGCATTTTTAAA-CTGATGGGCCTTTGGAAATC
66 ATTAGGTAGCACTTATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGCCTTTGGAAATC
* *
5557966 CGACGATAACATAATCGGTTAATTACTT-ATATTGTTATTAATATTATCAACATATTAGGTAACG
131 CGACGATAACAAAATAGGTTAATTACTTAAT-TTGTTATTAATATTATCAACATATTAGGTAACG
*
5558030 CCTAAAATGTTACCAAAGTTTAAGCTGATAGC
195 CCTAAAATGTTACCAAAGTTTAAGCTGATAGA
* *
5558062 GCTTTAGAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGGATAATAACAT
1 GCTTTAGAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACAT
** * * * **
5558127 ATTAGGTAGTGCTTATGTAACGTAATAGATAGCGCCTTTTTAAAGCAT-TTGGGGTTTTGGAAAT
66 ATTAGGTAGCACTTATGTAACGTAATAGGTAGCGCATTTTTAAAGC-TGATGGGCCTTTGGAAAT
** *
5558191 CCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTTGTATTATCAACATATTAGGTACCG
130 CCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAATATTATCAACATATTAGGTAACG
*
5558256 CCTAAAATGTTACCACAGTTTAAGCTGATAGA
195 CCTAAAATGTTACCAAAGTTTAAGCTGATAGA
* * * *
5558288 GCCTTAGAAATCCGATGATAACATAACCGGTTAATTACTGGAAACGTTATCAAGCATAAAAACAT
1 GCTTTAGAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACAT
* * * * *
5558353 ATTAGGT-GACACTTATGTAACGTAATAAGTTGCGCATTATTAAAGTTGATGGGGCC-TTAGAAA
66 ATTAGGTAG-CACTTATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGAT-GGGCCTTTGGAAA
*
5558416 TCCGACGATAACAAAATAAGTTA
129 TCCGACGATAACAAAATAGGTTA
5558439 TGTTATCAGT
Statistics
Matches: 329, Mismatches: 42, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
225 98 0.30
226 225 0.68
227 6 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (226 bp):
GCTTTAGAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACAT
ATTAGGTAGCACTTATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGCCTTTGGAAATC
CGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAATATTATCAACATATTAGGTAACGC
CTAAAATGTTACCAAAGTTTAAGCTGATAGA
Found at i:5558683 original size:2 final size:2
Alignment explanation
Indices: 5558678--5558702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5558668 GTGTGTGTGT
5558678 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
5558703 TGGTATGTGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5558985 original size:2 final size:2
Alignment explanation
Indices: 5558940--5558977 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5558930 TAAGTATGGA
5558940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5558978 CGATATATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5560875 original size:21 final size:21
Alignment explanation
Indices: 5560851--5560903 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5560841 CACTTACCAA
5560851 AGTATTGATACATTTGTGTAT
1 AGTATTGATACATTTGTGTAT
5560872 AGTATTGATACATTTGTGTAT
1 AGTATTGATACATTTGTGTAT
* *
5560893 GGTATCGATAC
1 AGTATTGATAC
5560904 TTTCGAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (21 bp):
AGTATTGATACATTTGTGTAT
Found at i:5561738 original size:446 final size:447
Alignment explanation
Indices: 5560872--5561738 Score: 1328
Period size: 446 Copynumber: 1.9 Consensus size: 447
5560862 ATTTGTGTAT
* * * ** *
5560872 AGTATTGATACATTTGTGTATGGTATCGATACTTTCGAGATGTTTCATTTTTTTCAAAACTAATA
1 AGTATCGATACATTTATGTACGGTATCGATACTTTCGAGACATTTCATTTTTTTCAAAACCAATA
*
5560937 GCGATTTACCGGTTACATTGTATATTGAAACCGGTTTTATCAATTTTTAACCTTTTATATCATCA
66 GCGATTTACCGGTTA-ATTGTATATTGAAACCGATTTTATCAATTTTTAACCTTTTATATCATCA
* * * *
5561002 TGTATCGATACATGTATCATAGGTATCGAATACTTCCTACGTGTATCTAGTTTTGGGAAGCATAC
130 TGTATCGATAAATATATCATAGGTATCGAATACTTCCTACATGCATCTAGTTTTGGGAAGCATAC
*
5561067 TGGACAAAAAGTATCGATACATATACCAAAAGTATCGATACTTTATATAAACGTATTTTACCATT
195 TGGACAAAAAGTATCGATACATATACCAAAAGTATCGATACTTTATATAAAAGTATTTTACCATT
* * **
5561132 AAATCGGTATATTTTTACTGCTTACATTGTATATTTACCTATTACTTTAAAGTAATAGGTTTCGA
260 AAACCGATATATTTTTACAACTTACATTGTATATTTACCTATTACTTTAAAGTAATAGGTTTCGA
**
5561197 AGTTTTAAGAATCGATACTTTTCATATTTGTATCGATACTTTATAGGCGCAATTATGGAAACCGG
325 AGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCGCAATTATGGAAACCGG
* *
5561262 TTTTCTCAATTTTTTACCTGTTATGTTATTTTAAAATCGATACCATTACCCTTACATA
390 TTTTCTCAATTGTTTACCTGTTAAGTTATTTTAAAATCGATACCATTACCCTTACATA
* *
5561320 AGTATCGATACTTTTATGTACGGTATCTATACTTTCGAGACATTTCATTTTTTTTTCAAAACCAA
1 AGTATCGATACATTTATGTACGGTATCGATACTTTCGAGACATTTCA--TTTTTTTCAAAACCAA
* * * * * **
5561385 TAGCTATTTACC-GTT-TTTTTCATATTGAAATCGATTTTATCAATTTTTAACGTTTTATATTGT
64 TAGCGATTTACCGGTTAATTGT-ATATTGAAACCGATTTTATCAATTTTTAACCTTTTATATCAT
* *
5561448 CTTGTATCGATAAATATGTCATAGGTATCG-ATACTTCCTACATGCATCTAGTTTTGGGAAGCAT
128 CATGTATCGATAAATATATCATAGGTATCGAATACTTCCTACATGCATCTAGTTTTGGGAAGCAT
* * *
5561512 ACTGGATAAAAAGTATCGATACATATACCAAAAGTATTGATACTTTCTATAAAAGTATTTTACCA
193 ACTGGACAAAAAGTATCGATACATATACCAAAAGTATCGATACTTTATATAAAAGTATTTTACCA
*
5561577 TTAAACCGATATA-TTTTACAACTTACATTGTATATTTACCTATTACTTTAAAGTAATCGGTTTC
258 TTAAACCGATATATTTTTACAACTTACATTGTATATTTACCTATTACTTTAAAGTAATAGGTTTC
* *
5561641 GAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCGTAGTTATGGAAACC
323 GAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCGCAATTATGGAAACC
*
5561706 GGTTTTGTCAATTGTTTACCTGTTAAGTTATTT
388 GGTTTTCTCAATTGTTTACCTGTTAAGTTATTT
5561739 ATATTGAAAC
Statistics
Matches: 378, Mismatches: 38, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
446 139 0.37
447 107 0.28
448 103 0.27
449 3 0.01
450 26 0.07
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (447 bp):
AGTATCGATACATTTATGTACGGTATCGATACTTTCGAGACATTTCATTTTTTTCAAAACCAATA
GCGATTTACCGGTTAATTGTATATTGAAACCGATTTTATCAATTTTTAACCTTTTATATCATCAT
GTATCGATAAATATATCATAGGTATCGAATACTTCCTACATGCATCTAGTTTTGGGAAGCATACT
GGACAAAAAGTATCGATACATATACCAAAAGTATCGATACTTTATATAAAAGTATTTTACCATTA
AACCGATATATTTTTACAACTTACATTGTATATTTACCTATTACTTTAAAGTAATAGGTTTCGAA
GTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTATAGGCGCAATTATGGAAACCGGT
TTTCTCAATTGTTTACCTGTTAAGTTATTTTAAAATCGATACCATTACCCTTACATA
Found at i:5563234 original size:24 final size:25
Alignment explanation
Indices: 5563203--5563266 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
5563193 AGTGGAGCCA
5563203 AAATTTAAATTGAAATTCAAAC-TC
1 AAATTTAAATTGAAATTCAAACTTC
*
5563227 AAATTTAAATTTAAATTCAAACTTC
1 AAATTTAAATTGAAATTCAAACTTC
**
5563252 -AATCAAAATTGAAAT
1 AAATTTAAATTGAAAT
5563267 GAACATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (25 bp):
AAATTTAAATTGAAATTCAAACTTC
Found at i:5563236 original size:18 final size:18
Alignment explanation
Indices: 5563209--5563247 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5563199 GCCAAAATTT
5563209 AAATTGAAATTCAAACTC
1 AAATTGAAATTCAAACTC
* * *
5563227 AAATTTAAATTTAAATTC
1 AAATTGAAATTCAAACTC
5563245 AAA
1 AAA
5563248 CTTCAATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (18 bp):
AAATTGAAATTCAAACTC
Found at i:5565507 original size:2 final size:2
Alignment explanation
Indices: 5565500--5565527 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5565490 GAATCTGGAG
5565500 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
5565528 CATTCCCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5568337 original size:18 final size:18
Alignment explanation
Indices: 5568316--5568358 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
5568306 GTTGTTTATA
*
5568316 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
5568334 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
5568352 AAATAAA
1 AAATAAA
5568359 TAATATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:5572492 original size:23 final size:23
Alignment explanation
Indices: 5572444--5572493 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5572434 ATCAAGCACA
* *
5572444 ATAACATATTAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
5572467 ATAACGTAATAGGTAGCGCCTT-T
1 ATAACATAATAGGTAGCG-CTTAT
5572490 ATAA
1 ATAA
5572494 AGTTGATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:5572530 original size:118 final size:118
Alignment explanation
Indices: 5572400--5572660 Score: 375
Period size: 118 Copynumber: 2.2 Consensus size: 118
5572390 AAAAATATAC
*
5572400 ACGATAAAATAATCGGTTAATTACTTG-AAACATTATCAAGCACAATAACATATTAGGTAGTGCT
1 ACGATAACATAATCGGTTAATTACTTGAAAACATTATCAAGCACAATAACATATTAGGTAGTGCT
* *
5572464 TATATAACGTAATAGGTAGCGCCTTTATAAAGTTGATGAGG-CTTTAAAAATTCG
66 TATATAACGTAATAGGTAGCGCCTTT-TAAAGCTGATG-GGCCTTTAAAAATCCG
* *
5572518 ACGATAACATAATCAGTTAATTAC-TGAAAACATTATCAAGCATAATAACATATTAGGTAGTGCT
1 ACGATAACATAATCGGTTAATTACTTGAAAACATTATCAAGCACAATAACATATTAGGTAGTGCT
* * * **
5572582 TATATAATGTAATAGGTAGCGTCTTTTTAAGCTGATGGGCCTTTGGAAATCCG
66 TATATAACGTAATAGGTAGCGCCTTTTAAAGCTGATGGGCCTTTAAAAATCCG
* *
5572635 ATGATAACATAATCGGATAATTACTT
1 ACGATAACATAATCGGTTAATTACTT
5572661 ATATTGTTAT
Statistics
Matches: 127, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
116 2 0.02
117 42 0.33
118 83 0.65
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (118 bp):
ACGATAACATAATCGGTTAATTACTTGAAAACATTATCAAGCACAATAACATATTAGGTAGTGCT
TATATAACGTAATAGGTAGCGCCTTTTAAAGCTGATGGGCCTTTAAAAATCCG
Found at i:5572796 original size:108 final size:108
Alignment explanation
Indices: 5572681--5573027 Score: 290
Period size: 108 Copynumber: 3.1 Consensus size: 108
5572671 TAATATTATC
* *
5572681 AACATATTAGGTAACGCCTAAAATGTTATCA-AAGTTTAAGTTGATAGAGCCTTAAAAATCCGAC
1 AACATATTAGGTAACGCCTAAAATGTTACCACAA-TTTAAGTTGATAGAGCCTTAGAAATCCGAC
*
5572745 GATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAAT
65 GATAACATAACCGGTTAATTACTGGAAAAATTATCAAGCATAAT
* * * * * * * *
5572789 AACATATTAGGTAGCGCTTATGTAACGTAATATGTAGCACATTTTTAAAGCGTT--TGGGGCTTT
1 AACATATTAGGTAACGC----CTAA---AATGT-TACCACA-ATTT-AA--GTTGATAGAGCCTT
* * ** * *** **** *
5572852 AGAAATCCGATGATAACAAAATAGGTTAATTACT-TAATTTGTTAT-TTTTATTAT
54 AGAAATCCGACGATAACATAACCGGTTAATTACTGGAA-AAATTATCAAGCATAAT
*
5572906 CAACATATTAGGTAACGCCTAAAATGTTACCACAATTTAAGTTGATAGAACCTTAGAAATCCGAC
1 -AACATATTAGGTAACGCCTAAAATGTTACCACAATTTAAGTTGATAGAGCCTTAGAAATCCGAC
*
5572971 GATAACATAACCAGTTAATTACTGGAAAAATTATCAAGCATAAT
65 GATAACATAACCGGTTAATTACTGGAAAAATTATCAAGCATAAT
5573015 AACATATTAGGTA
1 AACATATTAGGTA
5573028 GTGCTTATGT
Statistics
Matches: 175, Mismatches: 45, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
106 3 0.02
108 69 0.39
109 9 0.05
110 6 0.03
111 4 0.02
112 3 0.02
114 3 0.02
115 4 0.02
116 4 0.02
117 10 0.06
118 57 0.33
120 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (108 bp):
AACATATTAGGTAACGCCTAAAATGTTACCACAATTTAAGTTGATAGAGCCTTAGAAATCCGACG
ATAACATAACCGGTTAATTACTGGAAAAATTATCAAGCATAAT
Found at i:5572950 original size:226 final size:226
Alignment explanation
Indices: 5572493--5573105 Score: 887
Period size: 226 Copynumber: 2.7 Consensus size: 226
5572483 CGCCTTTATA
* * * *
5572493 AAGTTGAT-GAGGCTTTAAAAATTCGACGATAACATAATCAGTTAATTACTGAAAACATTATCAA
1 AAGTTGATAGA-GCCTTAAAAATCCGACGATAACATAACCAGTTAATTACTGGAAACATTATCAA
* *
5572557 GCATAATAACATATTAGGTAGTGCTTATATAATGTAATAGGTAGCGTC-TTTTT-AAGCTGATGG
65 GCATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTAGC-ACATTTTTAAAGCTGATGG
* * * * *
5572620 GCCTTTGGAAATCCGATGATAACATAATCGGATAATTACTTATATTGTTATTAATATTATCAACA
129 GGCTTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTATATTGTTATTAATATTATCAACA
*
5572685 TATTAGGTAACGCCTAAAATGTTATCAAAGTTT
194 TATTAGGTAACGCCTAAAATGTTACCAAAGTTT
*
5572718 AAGTTGATAGAGCCTTAAAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAG
1 AAGTTGATAGAGCCTTAAAAATCCGACGATAACATAACCAGTTAATTACTGGAAACATTATCAAG
* * * *
5572783 CATAATAACATATTAGGTAGCGCTTATGTAACGTAATATGTAGCACATTTTTAAAGC-GTTTGGG
66 CATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTAGCACATTTTTAAAGCTG-ATGGG
**
5572847 GCTTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTA-ATTTGTTATTTTTATTATCAACA
130 GCTTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTATA-TTGTTATTAATATTATCAACA
5572911 TATTAGGTAACGCCTAAAATGTTACCACAA-TTT
194 TATTAGGTAACGCCTAAAATGTTACCA-AAGTTT
* * *
5572944 AAGTTGATAGAACCTTAGAAATCCGACGATAACATAACCAGTTAATTACTGGAAAAATTATCAAG
1 AAGTTGATAGAGCCTTAAAAATCCGACGATAACATAACCAGTTAATTACTGGAAACATTATCAAG
* * * *
5573009 CATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTTGCACATTATTAAAACTGATGGTG
66 CATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTAGCACATTTTTAAAGCTGATGGGG
* *
5573074 CCTTAGAAATCCGACGATAACAAAATAGGTTA
131 CTTTAGAAATCCGATGATAACAAAATAGGTTA
5573106 TGTTATCAAT
Statistics
Matches: 348, Mismatches: 33, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
224 1 0.00
225 104 0.30
226 240 0.69
227 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (226 bp):
AAGTTGATAGAGCCTTAAAAATCCGACGATAACATAACCAGTTAATTACTGGAAACATTATCAAG
CATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTAGCACATTTTTAAAGCTGATGGGG
CTTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTATATTGTTATTAATATTATCAACATA
TTAGGTAACGCCTAAAATGTTACCAAAGTTT
Found at i:5573596 original size:2 final size:2
Alignment explanation
Indices: 5573589--5573622 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5573579 TAAGTATTGA
5573589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5573623 CGATACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5575652 original size:21 final size:22
Alignment explanation
Indices: 5575615--5575656 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5575605 TTTAACCTTT
*
5575615 TATATCATCATGTATCGATACA
1 TATATCATCAGGTATCGATACA
5575637 TATATCAT-AGGTATCGATAC
1 TATATCATCAGGTATCGATAC
5575657 TTCCTAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (22 bp):
TATATCATCAGGTATCGATACA
Found at i:5576018 original size:19 final size:20
Alignment explanation
Indices: 5575974--5576015 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5575964 GTATCGATAC
5575974 TTTCAAGACGTTTCATTTTT
1 TTTCAAGACGTTTCATTTTT
5575994 TTTCAAGACGTTTCATTTTT
1 TTTCAAGACGTTTCATTTTT
5576014 TT
1 TT
5576016 CAAAACCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTCAAGACGTTTCATTTTT
Found at i:5577877 original size:24 final size:24
Alignment explanation
Indices: 5577845--5577907 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
5577835 GTGGAGCCAA
5577845 AATTTAAATTTAAATTCAAACT-C
1 AATTTAAATTTAAATTCAAACTCC
5577868 AATTTGAAATTTAAATTCAAACTCC
1 AATTT-AAATTTAAATTCAAACTCC
* *
5577893 AATTAAAATTGAAAT
1 AATTTAAATTTAAAT
5577908 GAACATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 5 0.14
24 26 0.72
25 5 0.14
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (24 bp):
AATTTAAATTTAAATTCAAACTCC
Found at i:5581112 original size:200 final size:198
Alignment explanation
Indices: 5580739--5581229 Score: 660
Period size: 200 Copynumber: 2.4 Consensus size: 198
5580729 TATCAGTGTT
* * *
5580739 TTCATACTGGACAAAATGTATCGATACAACTTAAAAACGTATCGCTACTTTTTGTTTACTTATTC
1 TTCATATTGGACAAAA-GTATCGATACAACTTAAAAA-GTATCGATACTTTTTGTTTACCTATTC
* * * * * *
5580804 TCTTATTAAACCGGTATATTTTTAATGGTTACATTGTATATTTACCTATTACTTTATAATTATTG
64 TCTCATTAAACCGGTATATTTTTAACGGTTACATTGTAAAATTACCTATTACTTTATAATAATCG
* * * *
5580869 GTTTCGATGTTTTAAGTATCGATACTTATGATACATTTATCGATACTTTATGCATCCATCTCGTT
129 GTTTCGATATTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATCCATCTCGTT
*
5580934 TGGGA
194 TAGGA
* * * *
5580939 TTCATATTGGACTAAAAGTATCGATACTATTTAAACAAGTATTGATA-TTTTATGTATACCTATT
1 TTCATATTGGAC-AAAAGTATCGATACAACTTAAA-AAGTATCGATACTTTT-TGTTTACCTATT
* *
5581003 ATCTCATTAAACCGGTATATTTTTACCGGTTACATTGTAAAATTACCTATTACTTTATAATAATC
63 CTCTCATTAAACCGGTATATTTTTAACGGTTACATTGTAAAATTACCTATTACTTTATAATAATC
* ** *
5581068 GGTTTCGATATTTTAAGGATCGATACTTATCATACATGTATCGATATTTTATGTGTGCATCTCGT
128 GGTTTCGATATTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATCCATCTCGT
5581133 TTAGGA
193 TTAGGA
*
5581139 TTCATATTGGACAAAAAGTATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTC
1 TTCATATTGGAC-AAAAGTATCGATACAACTT-AAAAAGTATCGATACTTTTTGTTTACCTATTC
* *
5581204 TCTCATTAAACTGATATATGTTTTAA
64 TCTCATTAAACCGGTATAT-TTTTAA
5581230 GGATCCATAC
Statistics
Matches: 251, Mismatches: 34, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
199 4 0.02
200 229 0.91
201 18 0.07
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (198 bp):
TTCATATTGGACAAAAGTATCGATACAACTTAAAAAGTATCGATACTTTTTGTTTACCTATTCTC
TCATTAAACCGGTATATTTTTAACGGTTACATTGTAAAATTACCTATTACTTTATAATAATCGGT
TTCGATATTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGCATCCATCTCGTTTA
GGA
Found at i:5581374 original size:146 final size:146
Alignment explanation
Indices: 5581078--5581374 Score: 400
Period size: 146 Copynumber: 2.0 Consensus size: 146
5581068 GGTTTCGATA
* * * ** ** * *
5581078 TTTTAAGGATCGATACTTATCATACATGTATCGATATTTTATGTGTGCATCTCGTTTAGGATTCA
1 TTTTAAGGATCCATACATATCAAACATGTATCGATACATTATGCATCCATCTCATTTAGGATTCA
* * * * *
5581143 TATTGGACAAAAAGTATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTCTCTC
66 TATTGAAAAAAAAGCATCGATACAACTGAAAAAACTATCGATACTTTTTGTTAACCTATTCTCTC
5581208 ATTAAACTGATATATG
131 ATTAAACTGATATATG
* *
5581224 TTTTAAGGATCCATACATGTCAAACATGTATCGATACATTATGCATCCATCTCATTTGGGATTCA
1 TTTTAAGGATCCATACATATCAAACATGTATCGATACATTATGCATCCATCTCATTTAGGATTCA
* *
5581289 TACTTGAAAAAAAATGCATCGATACAACTGAAAAAAGTATCGATATTTTTTGTTAACCTATT-TC
66 TA-TTGAAAAAAAA-GCATCGATACAACTGAAAAAACTATCGATACTTTTTGTTAACCTATTCTC
5581353 TCATTAAACTGATATAT-
129 TCATTAAACTGATATATG
5581370 TTTTA
1 TTTTA
5581375 CCGGTTACAA
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
146 61 0.47
147 28 0.21
148 42 0.32
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (146 bp):
TTTTAAGGATCCATACATATCAAACATGTATCGATACATTATGCATCCATCTCATTTAGGATTCA
TATTGAAAAAAAAGCATCGATACAACTGAAAAAACTATCGATACTTTTTGTTAACCTATTCTCTC
ATTAAACTGATATATG
Found at i:5581408 original size:347 final size:333
Alignment explanation
Indices: 5580901--5581772 Score: 1081
Period size: 347 Copynumber: 2.6 Consensus size: 333
5580891 TACTTATGAT
* * * **
5580901 ACATTTATCGATACTTTATGCATCCATCTCGTTTGGGATTCATATTGGACTAAAA-GTATCGATA
1 ACATGTATCGATACATTATGCATCCATCTCATTTGGGATTCATATT-GAAAAAAATGTATCGATA
** * * *
5580965 CTATTTAAACAAGTATTGATATTTTATG-TATACCTATTATCTCATTAAACCGGTATATTTTTAC
65 C-AACTAAAAAAGTATTGATATTTTTTGTTA-ACCTATTATCTCATTAAACCGATATATTTTTAC
*
5581029 CGGTTACATTGTAAAATTACCTATTACTTTATAATAATCGGTTTCGATATTTTAAGGATCGATAC
128 CGGTTACAATGTAAAATTACCTATTACTTTATAATAATCGGTTTCGATATTTTAAGGATCGATAC
* * *
5581094 TTATCATACATGTATCGATATTTTATGTGTGCATCTCGTTTAGG-ATTCATATTGGACAAAAAGT
193 TTATCATACATGTATCAATACTTTATGTGTGCATCTCGTTT-GGAATTCATACTGGACAAAAAGT
* *
5581158 ATCGATACAACTTAAAAAACTATCGATACTTTTTGTTTACCTATTCTCTCATTAAACTGATATAT
257 ATCG-----A--T-----ACTATCGATACATTTTGTTTACCTATTCTCTCATTAAAATGATATAT
*
5581223 GTTTTAAGGATCCATACATGTCAA
310 GTTTTAAGGATCCATACATCTCAA
*
5581247 ACATGTATCGATACATTATGCATCCATCTCATTTGGGATTCATACTTGAAAAAAAATGCATCGAT
1 ACATGTATCGATACATTATGCATCCATCTCATTTGGGATTCATA-TTG-AAAAAAATGTATCGAT
* *
5581312 ACAACTGAAAAAAGTATCGATATTTTTTGTTAACCTATT-TCTCATTAAACTGATATATTTTTAC
64 ACAACT-AAAAAAGTATTGATATTTTTTGTTAACCTATTATCTCATTAAACCGATATATTTTTAC
* * * *
5581376 CGGTTACAATGTATATTTACCTATTACTTTATAATTATCGGTTTCGATGTTTTAAGGATCGATAC
128 CGGTTACAATGTAAAATTACCTATTACTTTATAATAATCGGTTTCGATATTTTAAGGATCGATAC
5581441 TTATCATACATGTATCAATACTTTATGTGTGCATCTCGTTTGGAATTCATACTGGACAAAAAGTA
193 TTATCATACATGTATCAATACTTTATGTGTGCATCTCGTTTGGAATTCATACTGGACAAAAAGTA
* *
5581506 TCGATACTATCGATACATTTTGTTTACCTATTCTCTCATTAAAATGGTATATGTTTTAAGGATCG
258 TCGATACTATCGATACATTTTGTTTACCTATTCTCTCATTAAAATGATATATGTTTTAAGGATCC
*
5581571 ATACGTCTCAA
323 ATACATCTCAA
* * * *
5581582 ACATGTATCGATACATTATGCGTCCATCTCATTTGGGACTCATATTGGAAAAAATGTATGGATAC
1 ACATGTATCGATACATTATGCATCCATCTCATTTGGGATTCATATTGAAAAAAATGTATCGATAC
* * * * * ** * *
5581647 AACTAAAAAAGTATTGATACTTTTTGTTTACCTATTCTCTCATTAAATCGGTA-ACAATATATCG
66 AACTAAAAAAGTATTGATATTTTTTGTTAACCTATTATCTCATTAAACCGATATA-TTTTTACCG
* * * * * * * *
5581711 CTTACATTGTAAATTTACCGATTACCTTCA-AATAATTGGTTTCGATGTTTTAAGAATCGATA
130 GTTACAATGTAAAATTACCTATTA-CTTTATAATAATCGGTTTCGATATTTTAAGGATCGATA
5581773 ATTTTAATAT
Statistics
Matches: 467, Mismatches: 50, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
332 30 0.06
333 86 0.18
334 7 0.01
335 107 0.23
340 1 0.00
342 1 0.00
346 44 0.09
347 154 0.33
348 35 0.07
349 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (333 bp):
ACATGTATCGATACATTATGCATCCATCTCATTTGGGATTCATATTGAAAAAAATGTATCGATAC
AACTAAAAAAGTATTGATATTTTTTGTTAACCTATTATCTCATTAAACCGATATATTTTTACCGG
TTACAATGTAAAATTACCTATTACTTTATAATAATCGGTTTCGATATTTTAAGGATCGATACTTA
TCATACATGTATCAATACTTTATGTGTGCATCTCGTTTGGAATTCATACTGGACAAAAAGTATCG
ATACTATCGATACATTTTGTTTACCTATTCTCTCATTAAAATGATATATGTTTTAAGGATCCATA
CATCTCAA
Found at i:5582265 original size:54 final size:54
Alignment explanation
Indices: 5582183--5582292 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
5582173 TGCATCAGAT
*
5582183 AATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGGTGAATCTAAC
1 AATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCTAAC
* *
5582237 AATGTTAAGCCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCTGAC
1 AATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCTAAC
5582291 AA
1 AA
5582293 ATTGGTTGGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (54 bp):
AATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCTAAC
Found at i:5584079 original size:15 final size:12
Alignment explanation
Indices: 5584030--5584083 Score: 90
Period size: 12 Copynumber: 4.5 Consensus size: 12
5584020 CATCCCCATA
5584030 CTTCCTTCTCTT
1 CTTCCTTCTCTT
5584042 CTTCCTTCTCTT
1 CTTCCTTCTCTT
5584054 CTTCCTTCTCTT
1 CTTCCTTCTCTT
* *
5584066 CTTCCTTATCCT
1 CTTCCTTCTCTT
5584078 CTTCCT
1 CTTCCT
5584084 CATCTGCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCCTTCTCTT
Found at i:5587991 original size:55 final size:56
Alignment explanation
Indices: 5587866--5588111 Score: 320
Period size: 57 Copynumber: 4.4 Consensus size: 56
5587856 ATGGCACTGA
* * *
5587866 GTGTGCAAAAAGTTAAGAAATTCATAAAGTTTTTATGAA-TTCTGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCAT-AATTTTTTATGAATTTCTATATGGACACTTT
*
5587922 GTGTGCAAAGAGTTAAGAAATTCA-AATTTTTTATGAATTTCTATATGGACACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTTTTATGAATTTCTATATGGACACTTT
** * **
5587977 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTGA
1 GTGTGCAAAAAGTTAAGAAATTCATAATTT-TTTATGAATTTCTATATGGACACTTT
*
5588034 GTGTGCAAAAAGTTAAGAAATTCATAATTTTTTTATGAATTTCTATATAAGA-ACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAA-TTTTTTATGAATTTCTATAT-GGACACTTT
* *
5588091 ATGTGCAAAAA-CTAAGAAATT
1 GTGTGCAAAAAGTTAAGAAATT
5588112 ATATGAATTT
Statistics
Matches: 167, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
54 12 0.07
55 38 0.23
56 37 0.22
57 76 0.46
58 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (56 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTTTTTATGAATTTCTATATGGACACTTT
Found at i:5588438 original size:68 final size:68
Alignment explanation
Indices: 5588285--5588692 Score: 543
Period size: 68 Copynumber: 6.0 Consensus size: 68
5588275 TAAAAGATTA
* * *
5588285 GAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGG---AGTACC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5588347 TTT
66 TTT
* * * * * * **
5588350 AAGGCCTAGCTATGCATTTGACAAAAAGGTGTCAATTATGCCAGTTATATGTAAGTCTAAGTGTA
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5588415 TTT
66 TTT
*
5588418 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTTAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5588483 TTT
66 TTT
* * *
5588486 GAGGCCTACCTGTCCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5588551 TTT
66 TTT
* * * *
5588554 GAGGCCTAGCTGTGAATTTGATAGAAAGGTGTCAATTATGCCAGATAGATGAAAGGCTAAGTGTC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5588619 TTT
66 TTT
* * * * * * * * *
5588622 GAGACCTAGCAGTGCATTTGACAGAAAGGTGTCAATCATACCAGTTAAAGGAAAGGTTAAATGTC
1 GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
5588687 TTT
66 TTT
5588690 GAG
1 GAG
5588693 TTAAAGACTA
Statistics
Matches: 298, Mismatches: 42, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
65 48 0.16
68 250 0.84
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (68 bp):
GAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:5588753 original size:22 final size:21
Alignment explanation
Indices: 5588728--5588802 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 21
5588718 ATAACGTTGT
5588728 ATAAAAGGCATGAAATGATGCC
1 ATAAAAGGCATGAAATGATG-C
* ** *
5588750 ATAAATGAAATGTATAAT-AGTGT
1 ATAAAAGGCATG-A-AATGA-TGC
5588773 ATAAAAAGGCATGAAATGATGAC
1 AT-AAAAGGCATGAAATGATG-C
5588796 ATAAAAG
1 ATAAAAG
5588803 AAATGTATAC
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 19 0.49
23 8 0.21
24 12 0.31
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.23
Consensus pattern (21 bp):
ATAAAAGGCATGAAATGATGC
Found at i:5588784 original size:46 final size:45
Alignment explanation
Indices: 5588725--5588852 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 45
5588715 TGCATAACGT
*
5588725 TGTATAAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAATGATGACATAAATGAAATGTATAATAG
* *
5588770 TGTATAAAAAGGCATGAAATGATGACATAAAAGAAATGTATACTAG
1 TGTAT-AAAAGGCATGAAATGATGACATAAATGAAATGTATAATAG
* * * * *
5588816 AGTATAAAAGGCATGAAAGGATGTCGTAATTGAAATG
1 TGTATAAAAGGCATGAAATGATGACATAAATGAAATG
5588853 CATATGGGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 32 0.44
46 41 0.56
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (45 bp):
TGTATAAAAGGCATGAAATGATGACATAAATGAAATGTATAATAG
Found at i:5588891 original size:45 final size:45
Alignment explanation
Indices: 5588825--5589047 Score: 322
Period size: 45 Copynumber: 5.0 Consensus size: 45
5588815 GAGTATAAAA
* *
5588825 GGCATGAAAGGATGTCGTAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5588870 GGCTTGAAATGATTCCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5588915 GGTATGAAAGGATGCCATAATTGAAATGCATATGAGTGTATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5588960 GACATGAAGGGATGCCATAATTGAAATGCATATGAGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5589005 GGCATGAAAGGATTCCATAATCGAAATGCATAT-GGTGCATTAT
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTAT
5589048 AAGTATGAAG
Statistics
Matches: 158, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 9 0.06
45 149 0.94
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:5593277 original size:24 final size:24
Alignment explanation
Indices: 5593233--5593283 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5593223 GGCACCCAAG
* **
5593233 AATATAATTTTTATTTTAATAA-A
1 AATATAATTTTAATTGAAATAACA
5593256 AATATTAATTTTAATTGAAATAACA
1 AATA-TAATTTTAATTGAAATAACA
5593281 AAT
1 AAT
5593284 TTACGATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
AATATAATTTTAATTGAAATAACA
Found at i:5595916 original size:20 final size:20
Alignment explanation
Indices: 5595879--5595917 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5595869 TTTCCACCAC
*
5595879 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
5595899 ATGCATCTATATGATTCTA
1 ATGCAACTAAATGATTCTA
5595918 TATGTGCTTT
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:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:5596111 original size:16 final size:16
Alignment explanation
Indices: 5596088--5596127 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
5596078 ACAATTAATA
5596088 TATATTTAAAATATTAT
1 TATATTTAAAATA-TAT
*
5596105 T-TATTTAAAGTATAT
1 TATATTTAAAATATAT
5596120 TATATTTA
1 TATATTTA
5596128 GTAAGCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTTAAAATATAT
Found at i:5602574 original size:61 final size:62
Alignment explanation
Indices: 5602500--5602619 Score: 140
Period size: 62 Copynumber: 2.0 Consensus size: 62
5602490 AAAATAAAAG
* * *
5602500 AAATGTCAAAT-AAAAT-TTAAATTGAAAAAA-ATAAATCAAA-GAAGGAAATATTAAATTTTAA
1 AAATGTCAAATAAAAATGTTAAA-AGAAAAAATA-AAAT-AAATAAAGAAAATATTAAATTTTAA
* *
5602561 AAATGTTATATAAAAATGTTAAAAGAAAAAATAAAATAAATAAAGAAAATATTAAATTT
1 AAATGTCAAATAAAAATGTTAAAAGAAAAAATAAAATAAATAAAGAAAATATTAAATTT
5602620 CAGAAAAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
61 12 0.24
62 32 0.64
63 6 0.12
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.28
Consensus pattern (62 bp):
AAATGTCAAATAAAAATGTTAAAAGAAAAAATAAAATAAATAAAGAAAATATTAAATTTTAA
Found at i:5602677 original size:36 final size:34
Alignment explanation
Indices: 5602623--5602726 Score: 99
Period size: 35 Copynumber: 3.1 Consensus size: 34
5602613 TAAATTTCAG
* * *
5602623 AAAAGAAAAA-AATAA-AATATGAAAAAA-TGTT
1 AAAAGAAAAATAAAAACAAAATAAAAAAAGTGTT
**
5602654 AAAAGAGAAAATAAAAACAAAATAAAAAAGAAGTGGG
1 AAAAGA-AAAATAAAAACAAAAT-AAAAA-AAGTGTT
*
5602691 AAAATAAAAAT-AAAACAAAATAAAAAAAGTGTT
1 AAAAGAAAAATAAAAACAAAATAAAAAAAGTGTT
5602724 AAA
1 AAA
5602727 TTTTAAAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
31 6 0.10
32 4 0.07
33 12 0.20
34 9 0.15
35 14 0.24
36 7 0.12
37 7 0.12
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (34 bp):
AAAAGAAAAATAAAAACAAAATAAAAAAAGTGTT
Found at i:5612235 original size:226 final size:224
Alignment explanation
Indices: 5611774--5612366 Score: 719
Period size: 226 Copynumber: 2.6 Consensus size: 224
5611764 GGGGCTTTGA
* * * *
5611774 AAATACGACGATAACATAATCGGTTAATTACTGGAAACATTATCAAGCATATTAACATATTAGAT
1 AAATCCGACGATAACATAATCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGT
** * * * * * **
5611839 AATGCTTATATAACGTAATAGGTAGTGCCTTTTTCAGCTGATGGGGATTTAGAAATTTAAAGATA
66 AGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAGCTGATAGGGATTGAGAAATCCAAAGATA
* ** * *
5611904 ACATAATCTGTTAAATACTTATTTGTTATTAATATTATCAATATATTAGGTAACGCCTAAAATGT
131 ACAAAATAGGTTAAATACTTATTTATTATTAATATTATCAACATATTAGGTAACGCCTAAAATGT
5611969 TACCAAAGTTTAAGCTGATAGAGCCTTAG
196 TACCAAAGTTTAAGCTGATAGAGCCTTAG
*
5611998 AAATCCGACGATAACATAATCGGTTAATTACTAAAAACATTATCAAGCATAATAACATATTAGGT
1 AAATCCGACGATAACATAATCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGT
* * * * * *
5612063 AGCGCTAATGTAACGTAATAGGTAGCGCTTTTTTAAAGC-GTTTAGGGCTGTGA-AAATCCGATG
66 AGCGCTTATGTAACGTAATAGGTAGCGCCTTTTT-AAGCTG-ATAGGGAT-TGAGAAATCCAAAG
* * **
5612126 ATAACAAAATAGGTTAATTATTTAATTTATTATTTGTATTATCAACATATTAGGTAACGCCTAAA
128 ATAACAAAATAGGTTAAATACTT-ATTTATTATTAATATTATCAACATATTAGGTAACGCCTAAA
5612191 ATGTTACCACAA-TTTAAGCTGATAGAGCCTTAG
192 ATGTTACCA-AAGTTTAAGCTGATAGAGCCTTAG
* * *
5612224 AAATCCGACGATAACATAACCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGC
1 AAATCCGACGATAACATAATCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGT
* * * * * * * *
5612289 AGCACTTATGTAACATAATAGGT-GCACATTATTAAAGCTGATGGGGCCTT-AGAAATCCAACGA
66 AGCGCTTATGTAACGTAATAGGTAGCGCCTT-TTTAAGCTGATAGGG-ATTGAGAAATCCAAAGA
*
5612352 TAAAAAAATAGGTTA
129 TAACAAAATAGGTTA
5612367 TGTTATCAGT
Statistics
Matches: 316, Mismatches: 44, Indels: 17
0.84 0.12 0.05
Matches are distributed among these distances:
224 90 0.28
225 69 0.22
226 155 0.49
227 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (224 bp):
AAATCCGACGATAACATAATCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGT
AGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAGCTGATAGGGATTGAGAAATCCAAAGATA
ACAAAATAGGTTAAATACTTATTTATTATTAATATTATCAACATATTAGGTAACGCCTAAAATGT
TACCAAAGTTTAAGCTGATAGAGCCTTAG
Found at i:5612846 original size:2 final size:2
Alignment explanation
Indices: 5612839--5612876 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5612829 TAAGTATGGA
5612839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5612877 CGATACATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5617027 original size:24 final size:24
Alignment explanation
Indices: 5617000--5617063 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
5616990 AGTGGAGCTG
*
5617000 AAATTTAAATTTAAATTCAAACTC
1 AAATTAAAATTTAAATTCAAACTC
*
5617024 AAATTGAAATTTAAATTCAAACTC
1 AAATTAAAATTTAAATTCAAACTC
* *
5617048 CAATTAAAATTGAAAT
1 AAATTAAAATTTAAAT
5617064 GAACATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (24 bp):
AAATTAAAATTTAAATTCAAACTC
Found at i:5617033 original size:18 final size:18
Alignment explanation
Indices: 5617006--5617044 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5616996 GCTGAAATTT
*
5617006 AAATTTAAATTCAAACTC
1 AAATTGAAATTCAAACTC
* *
5617024 AAATTGAAATTTAAATTC
1 AAATTGAAATTCAAACTC
5617042 AAA
1 AAA
5617045 CTCCAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (18 bp):
AAATTGAAATTCAAACTC
Found at i:5617034 original size:30 final size:30
Alignment explanation
Indices: 5616998--5617063 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
5616988 ATAGTGGAGC
* * *
5616998 TGAAATTTAAATTTAAATTCAAACTCAAAT
1 TGAAATTTAAATTCAAACTCAAACTAAAAT
* *
5617028 TGAAATTTAAATTCAAACTCCAATTAAAAT
1 TGAAATTTAAATTCAAACTCAAACTAAAAT
5617058 TGAAAT
1 TGAAAT
5617064 GAACATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.35
Consensus pattern (30 bp):
TGAAATTTAAATTCAAACTCAAACTAAAAT
Found at i:5618348 original size:13 final size:13
Alignment explanation
Indices: 5618330--5618407 Score: 102
Period size: 13 Copynumber: 6.0 Consensus size: 13
5618320 GTCATAAATC
* *
5618330 TATGACGTGTATT
1 TATGACGCGCATT
*
5618343 TATGACACGCATT
1 TATGACGCGCATT
*
5618356 TATGATGCGCATT
1 TATGACGCGCATT
*
5618369 TATGACACGCATT
1 TATGACGCGCATT
5618382 TATGACGCGCATT
1 TATGACGCGCATT
*
5618395 TATGTCGCGCATT
1 TATGACGCGCATT
5618408 GCGCGTCATT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:5618557 original size:2 final size:2
Alignment explanation
Indices: 5618550--5618592 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5618540 TGTCGTAAAT
*
5618550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5618592 T
1 T
5618593 TGATAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.