Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 10 of 19
Found at i:1168891 original size:13 final size:13
Alignment explanation
Indices: 1168870--1168899 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1168860 TTTTTTTTGA
*
1168870 AATATTTGTATTT
1 AATACTTGTATTT
1168883 AATACTTGTATTT
1 AATACTTGTATTT
1168896 AATA
1 AATA
1168900 TATATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (13 bp):
AATACTTGTATTT
Found at i:1169707 original size:27 final size:26
Alignment explanation
Indices: 1169669--1169736 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
1169659 TTTATGATAT
* *
1169669 AAAT-TATTAATATATGATAATTTATA
1 AAATATATAAATATATGAT-ATTAATA
1169695 TAAATATA-AAATATTATGATATTAATA
1 -AAATATATAAATA-TATGATATTAATA
1169722 AAATATATAAATATA
1 AAATATATAAATATA
1169737 ATATAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 9 0.25
27 19 0.53
28 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
AAATATATAAATATATGATATTAATA
Found at i:1169735 original size:19 final size:19
Alignment explanation
Indices: 1169700--1169758 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1169690 TTATATAAAT
*
1169700 ATAAAATAT-TATGATATTA
1 ATAAAATATATA-AATATTA
1169719 ATAAAATATATAAATA-TA
1 ATAAAATATATAAATATTA
*
1169737 ATATAAATATACAAATTATTA
1 ATA-AAATATATAAA-TATTA
1169758 A
1 A
1169759 ATACTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.15
19 22 0.65
20 4 0.12
21 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAAATATATAAATATTA
Found at i:1169745 original size:24 final size:25
Alignment explanation
Indices: 1169696--1169745 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
1169686 TAATTTATAT
*
1169696 AAATATAAAATATTATGATATTAATA
1 AAATATAAAATATTA-GATATAAATA
1169722 AAATATATAAATA-TA-ATATAAATA
1 AAATATA-AAATATTAGATATAAATA
1169746 TACAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 8 0.36
26 9 0.41
27 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATATAAAATATTAGATATAAATA
Found at i:1170007 original size:15 final size:15
Alignment explanation
Indices: 1169987--1170016 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1169977 TTATTATAAA
*
1169987 AATATAAATATTAAT
1 AATATAAAAATTAAT
1170002 AATATAAAAATTAAT
1 AATATAAAAATTAAT
1170017 TTTTATATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAAAAATTAAT
Found at i:1176732 original size:2 final size:2
Alignment explanation
Indices: 1176719--1176755 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1176709 AAACATTTAA
* *
1176719 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1176756 AATTCTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1176997 original size:11 final size:12
Alignment explanation
Indices: 1176976--1177026 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
1176966 ATAAAATATT
1176976 TATTATATTTAA
1 TATTATATTTAA
1176988 TATT-TATTTAA
1 TATTATATTTAA
* *
1176999 TATTAAAATTAA
1 TATTATATTTAA
1177011 TTATTTAATATTTAA
1 -TA-TT-ATATTTAA
1177026 T
1 T
1177027 TTTTTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 11 0.35
12 9 0.29
13 2 0.06
14 3 0.10
15 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:1177404 original size:17 final size:17
Alignment explanation
Indices: 1177384--1177417 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1177374 AAATTAAATT
1177384 AATATTGAA-ATATTAAA
1 AATA-TGAATATATTAAA
1177401 AATATGAATATATTAAA
1 AATATGAATATATTAAA
1177418 TTGATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
AATATGAATATATTAAA
Found at i:1177957 original size:16 final size:19
Alignment explanation
Indices: 1177931--1177968 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1177921 ATTCAAATGG
1177931 AATCGAA-TTTTATTTT-T
1 AATCGAATTTTTATTTTAT
1177948 AATC-AATTTTTATTTTAT
1 AATCGAATTTTTATTTTAT
1177966 AAT
1 AAT
1177969 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 13 0.68
18 4 0.21
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (19 bp):
AATCGAATTTTTATTTTAT
Found at i:1178836 original size:31 final size:33
Alignment explanation
Indices: 1178789--1178858 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
1178779 TAATTTTTTA
*
1178789 TATATTTAAATAAATTTTAATA-A-TT-AATCATT
1 TATA-TTAAATAAATTTAAATATATTTAAAT-ATT
*
1178821 TATATTACATAAATTTAAATATATTTAAATATT
1 TATATTAAATAAATTTAAATATATTTAAATATT
1178854 TATAT
1 TATAT
1178859 CATATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 15 0.45
32 5 0.15
33 10 0.30
34 3 0.09
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATTAAATAAATTTAAATATATTTAAATATT
Found at i:1178879 original size:18 final size:20
Alignment explanation
Indices: 1178852--1178896 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1178842 TATTTAAATA
1178852 TTTA-TATCATA-TAT-TTT
1 TTTATTATCATATTATATTT
1178869 TTTATTATCATATTATATTT
1 TTTATTATCATATTATATTT
*
1178889 TATATTAT
1 TTTATTAT
1178897 ATTTATACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 7 0.29
19 3 0.12
20 10 0.42
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTATCATATTATATTT
Found at i:1179405 original size:26 final size:25
Alignment explanation
Indices: 1179368--1179430 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
1179358 ACATGACATA
*
1179368 AATATATAAATATTTAAAATTTATAT
1 AATATATTAATATTTAAAA-TTATAT
* *
1179394 AATATATTAATAATTAATATTATAT
1 AATATATTAATATTTAAAATTATAT
*
1179419 AA-ATTTTAATAT
1 AATATATTAATAT
1179431 AAATATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 8 0.25
25 8 0.25
26 16 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATATTAATATTTAAAATTATAT
Found at i:1179408 original size:20 final size:20
Alignment explanation
Indices: 1179370--1179419 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1179360 ATGACATAAA
1179370 TATATAA-ATATTTAAAATT
1 TATATAATATATTTAAAATT
1179389 TATATAATATA-TTAATAATT
1 TATATAATATATTTAA-AATT
* *
1179409 AATATTATATA
1 TATATAATATA
1179420 AATTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAATATATTTAAAATT
Found at i:1181412 original size:3 final size:3
Alignment explanation
Indices: 1181404--1181445 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1181394 CAGTTTGTGA
1181404 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1181446 TATGGACTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1183946 original size:2 final size:2
Alignment explanation
Indices: 1183939--1183975 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1183929 GAAGAAAACA
1183939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1183976 AACCACCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1187811 original size:9 final size:9
Alignment explanation
Indices: 1187797--1187829 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1187787 ATTTATATTT
1187797 TATAAAAAA
1 TATAAAAAA
1187806 TATAAAAAA
1 TATAAAAAA
1187815 TATATAAAAA
1 TATA-AAAAA
1187825 T-TAAA
1 TATAAA
1187830 TAAAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 15 0.65
10 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TATAAAAAA
Found at i:1187954 original size:18 final size:20
Alignment explanation
Indices: 1187931--1187967 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1187921 CTTAAATCAT
1187931 TCAATTTTG-TTA-GTTTAA
1 TCAATTTTGATTATGTTTAA
1187949 TCAATTTTGATTATGTTTA
1 TCAATTTTGATTATGTTTA
1187968 TATTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (20 bp):
TCAATTTTGATTATGTTTAA
Found at i:1188002 original size:16 final size:15
Alignment explanation
Indices: 1187966--1188011 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1187956 TGATTATGTT
1187966 TATATTAT-TATATA
1 TATATTATATATATA
* *
1187980 AAAATTATATATTATA
1 TATATTATATA-TATA
1187996 TATATTATAT-TATA
1 TATATTATATATATA
1188010 TA
1 TA
1188012 ATTTTAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.46
15 2 0.08
16 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:1188570 original size:20 final size:19
Alignment explanation
Indices: 1188547--1188588 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1188537 TTTTATTTAA
1188547 ATTTAAATTCAGTTTA-ATTT
1 ATTTAAATT-A-TTTATATTT
1188567 ATTTAAATTATTTATATTT
1 ATTTAAATTATTTATATTT
1188586 ATT
1 ATT
1188589 ATTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAAATTATTTATATTT
Found at i:1188702 original size:20 final size:20
Alignment explanation
Indices: 1188649--1188728 Score: 71
Period size: 20 Copynumber: 4.1 Consensus size: 20
1188639 TATTTTATAA
*
1188649 TTAAATTTAAATAAA-AATAT
1 TTAAATTTATATAAATAA-AT
* *
1188669 TTATAA-TTATTATATATTAAT
1 TTA-AATTTA-TATAAATAAAT
1188690 TTAAATTTATATAAATAAAT
1 TTAAATTTATATAAATAAAT
1188710 TTAAA-TTA-ATAAA-AAAT
1 TTAAATTTATATAAATAAAT
1188727 TT
1 TT
1188729 GTTCAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
17 6 0.12
18 5 0.10
19 3 0.06
20 22 0.43
21 14 0.27
22 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATTTATATAAATAAAT
Found at i:1188990 original size:19 final size:21
Alignment explanation
Indices: 1188957--1189001 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1188947 TGATCGAGTT
1188957 ATTTATTTAAATATTT-AAAA
1 ATTTATTTAAATATTTAAAAA
1188977 ATTTATTT-AATATTTAAAAA
1 ATTTATTTAAATATTTAAAAA
1188997 ATTTA
1 ATTTA
1189002 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTATTTAAATATTTAAAAA
Found at i:1189049 original size:6 final size:6
Alignment explanation
Indices: 1189038--1189063 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1189028 ATTTTAAAAA
1189038 AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
1189064 TTTGACCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:1189750 original size:27 final size:27
Alignment explanation
Indices: 1189720--1189888 Score: 102
Period size: 27 Copynumber: 6.2 Consensus size: 27
1189710 ATTTAATCGA
*
1189720 TATATTTAATAATTTATATATTTTTAT
1 TATATTTAATAATTTATATATTTATAT
* *
1189747 TATATTTATCTATTTTAT-TATATTATAAT
1 TATATTTA-ATAATTTATATAT-TTAT-AT
* *
1189776 TATATTTAA-ATTTTTTATATTTATAT
1 TATATTTAATAATTTATATATTTATAT
*
1189802 TA-ATTTTAATATATTAATA-ATTTATAT
1 TATA-TTTAATA-ATTTATATATTTATAT
* ** *
1189829 TATATAAATT-TTAAAATATATTTTTATAT
1 TATAT---TTAATAATTTATATATTTATAT
*
1189858 TATATTT--TTA-TTATATTATTTATAT
1 TATATTTAATAATTTATA-TATTTATAT
1189883 TATATT
1 TATATT
1189889 GATATCATAA
Statistics
Matches: 113, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
24 4 0.04
25 17 0.15
26 11 0.10
27 33 0.29
28 22 0.19
29 24 0.21
30 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (27 bp):
TATATTTAATAATTTATATATTTATAT
Found at i:1189763 original size:18 final size:19
Alignment explanation
Indices: 1189731--1189833 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 19
1189721 ATATTTAATA
1189731 ATTTATATATTTTTATTAT
1 ATTTATATATTTTTATTAT
*
1189750 ATTTATCTA-TTTTATTAT
1 ATTTATATATTTTTATTAT
*
1189768 ATTATAATTATATTTAAATTTTTTAT
1 ATT-T-A-TATA-TT---TTTATTAT
* *
1189794 ATTTATATTAATTTTAATAT
1 ATTTATA-TATTTTTATTAT
* *
1189814 ATTAATA-ATTTATATTAT
1 ATTTATATATTTTTATTAT
1189832 AT
1 AT
1189834 AAATTTTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
18 22 0.34
19 9 0.14
20 13 0.20
21 3 0.05
23 4 0.06
24 3 0.05
25 1 0.02
26 10 0.15
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATATATTTTTATTAT
Found at i:1189765 original size:5 final size:5
Alignment explanation
Indices: 1189744--1189911 Score: 79
Period size: 5 Copynumber: 34.2 Consensus size: 5
1189734 TATATATTTT
*
1189744 TATTA TATT- TATCTA T-TT- TATTA TATTA TAATTA TATTTA AATT-
1 TATTA TATTA TAT-TA TATTA TATTA TATTA T-ATTA TA-TTA TATTA
* * * * *
1189788 TTTTA TATTTA TATTA -ATTT TAATA TATTA -ATAA T-TTA TATTA TATAAA
1 TATTA TA-TTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA
* * * *
1189837 TTTTA AAATA TATT- T-TTA TATTA TATTTT TATTA TATTA T-TTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TA-TTA TATTA TATTA TATTA TATTA
* *
1189885 TATTGA TATCA TAATA T-TTAA TATTA T
1 TATT-A TATTA TATTA TATT-A TATTA T
1189912 CAAATCTATT
Statistics
Matches: 120, Mismatches: 24, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
3 3 0.03
4 24 0.20
5 65 0.54
6 28 0.23
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:1189799 original size:44 final size:49
Alignment explanation
Indices: 1189719--1189829 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 49
1189709 TATTTAATCG
*
1189719 ATATATTTAATAATTTATA--T-ATTTTTATTATATTTAT-CT-ATTTTA
1 ATATA-TTAATAATTTATATTTAAATTTTATTATATTTATACTAATTTTA
* *
1189764 TTATATT-ATAA-TTATATTTAAATTTT-TTATATTTATATTAATTTTA
1 ATATATTAATAATTTATATTTAAATTTTATTATATTTATACTAATTTTA
1189810 ATATATTAATAATTTATATT
1 ATATATTAATAATTTATATT
1189830 ATATAAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
42 5 0.09
43 4 0.07
44 13 0.24
45 10 0.18
46 12 0.22
47 4 0.07
48 7 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (49 bp):
ATATATTAATAATTTATATTTAAATTTTATTATATTTATACTAATTTTA
Found at i:1189816 original size:14 final size:14
Alignment explanation
Indices: 1189797--1189888 Score: 50
Period size: 14 Copynumber: 6.4 Consensus size: 14
1189787 TTTTTATATT
1189797 TATATTAATTTTAA
1 TATATTAATTTTAA
1189811 TATATTAATAATTTATA
1 TATATTAAT--TTTA-A
*
1189828 TTATATAAATTTTAA
1 -TATATTAATTTTAA
*
1189843 AATA-T-ATTTT--
1 TATATTAATTTTAA
*
1189853 TATATTATATTTTTAT
1 TATATTA-A-TTTTAA
*
1189869 TATATT-ATTTATAT
1 TATATTAATTT-TAA
1189883 TATATT
1 TATATT
1189889 GATATCATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 22
0.71 0.04 0.25
Matches are distributed among these distances:
10 3 0.05
11 1 0.02
12 5 0.08
13 4 0.06
14 26 0.41
15 1 0.02
16 14 0.22
17 1 0.02
18 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTAATTTTAA
Found at i:1189832 original size:32 final size:29
Alignment explanation
Indices: 1189789--1189888 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 29
1189779 ATTTAAATTT
*
1189789 TTTATATTTATATTAATTTTAATATATTAATAA
1 TTTATA-TTATATTAATTTTAAAATA-T-AT-A
* *
1189822 TTTATATTATATAAATTTTAAAATATATT
1 TTTATATTATATTAATTTTAAAATATATA
**
1189851 TTTATATTATA-T--TTTTATTATAT-TA
1 TTTATATTATATTAATTTTAAAATATATA
1189876 TTTATATTATATT
1 TTTATATTATATT
1189889 GATATCATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.20
26 10 0.17
29 11 0.19
30 2 0.03
31 1 0.02
32 17 0.29
33 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATATTATATTAATTTTAAAATATATA
Found at i:1189888 original size:11 final size:11
Alignment explanation
Indices: 1189736--1189893 Score: 75
Period size: 11 Copynumber: 14.5 Consensus size: 11
1189726 TAATAATTTA
*
1189736 TATATTTTTAT
1 TATATTTATAT
1189747 TATATTTATCTAT
1 TATATTTA--TAT
*
1189760 TTTA-TTATAT
1 TATATTTATAT
*
1189770 TATAATTATATT
1 TATATTTATA-T
*
1189782 TAAATTT-T-T
1 TATATTTATAT
1189791 TATATTTATAT
1 TATATTTATAT
*
1189802 TA-ATTT-TAA
1 TATATTTATAT
*
1189811 TATATTAATAAT
1 TATATTTAT-AT
1189823 T-TATATTATA-
1 TATAT-TTATAT
* *
1189833 TAAATTTTAAAAT
1 TATA-TTT-ATAT
*
1189846 ATATTTTTATAT
1 -TATATTTATAT
*
1189858 TATATTTTTAT
1 TATATTTATAT
1189869 TATA-TTAT-T
1 TATATTTATAT
1189878 TATA-TTATAT
1 TATATTTATAT
1189888 TGATAT
1 T-ATAT
1189894 CATAATATTT
Statistics
Matches: 111, Mismatches: 18, Indels: 35
0.68 0.11 0.21
Matches are distributed among these distances:
9 20 0.18
10 20 0.18
11 40 0.36
12 20 0.18
13 9 0.08
14 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1191403 original size:14 final size:14
Alignment explanation
Indices: 1191386--1191427 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 14
1191376 CCTATTTTAT
1191386 AATTTATATAATAA
1 AATTTATATAATAA
1191400 AATTATTAATATAATAA
1 AA-T-TT-ATATAATAA
1191417 AATTTATATAA
1 AATTTATATAA
1191428 ACATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 3 0.12
17 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTATATAATAA
Found at i:1191413 original size:17 final size:17
Alignment explanation
Indices: 1191391--1191487 Score: 69
Period size: 17 Copynumber: 5.7 Consensus size: 17
1191381 TTTATAATTT
1191391 ATATAATAAAATTATTA
1 ATATAATAAAATTATTA
1191408 ATATAATAAAATTTATATA
1 ATATAATAAAA-TTAT-TA
*
1191427 A-A-CATAAAATATATTA
1 ATATAATAAAAT-TATTA
* *
1191443 A-A-CATATAATTA-TA
1 ATATAATAAAATTATTA
* *
1191457 ATATTATAAAATATATAA
1 ATATAATAAAAT-TATTA
1191475 ATATAATATAAAT
1 ATATAATA-AAAT
1191488 ATATAAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 18 0.27
17 22 0.33
18 13 0.20
19 7 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAATAAAATTATTA
Found at i:1191464 original size:40 final size:41
Alignment explanation
Indices: 1191408--1191498 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 41
1191398 AAAATTATTA
*
1191408 ATATAA-TAAAATTTATATAAACATA-AAATAT-AT-TAAAC
1 ATATAATTATAATTTATA-AAACATATAAATATAATATAAAC
* *
1191446 ATATAATTATAATATTATAAAATATATAAATATAATATAAAT
1 ATATAATTATAAT-TTATAAAACATATAAATATAATATAAAC
1191488 ATATAAATTAT
1 ATAT-AATTAT
1191499 TAAAAATTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 6 0.14
39 11 0.25
40 11 0.25
41 2 0.05
42 8 0.18
43 6 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (41 bp):
ATATAATTATAATTTATAAAACATATAAATATAATATAAAC
Found at i:1191912 original size:20 final size:20
Alignment explanation
Indices: 1191873--1191912 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1191863 AATTCAAATT
* **
1191873 TATTTTAAAATTTATGTTAA
1 TATTTAAAAATTTAAATTAA
1191893 TATTTAAAAATTTAAATTAA
1 TATTTAAAAATTTAAATTAA
1191913 AAATTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTAAAAATTTAAATTAA
Found at i:1192591 original size:49 final size:49
Alignment explanation
Indices: 1192496--1192591 Score: 108
Period size: 49 Copynumber: 2.0 Consensus size: 49
1192486 AATTCATAAT
* * * *
1192496 TAATAAAAATTTTAAAAAATTATTTTTTATATTAATATATATATTTTTA
1 TAATAAAAATTTAAAAAAAATATTTCTTATATAAATATATATATTTTTA
1192545 TAAT-AAAATTTAAATAAAAATATTTCTTATTACTAAATAT-TA-ATTTT
1 TAATAAAAATTTAAA-AAAAATATTTCTTA-TA-TAAATATATATATTTT
1192592 GATCAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
48 9 0.22
49 21 0.52
50 4 0.10
51 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (49 bp):
TAATAAAAATTTAAAAAAAATATTTCTTATATAAATATATATATTTTTA
Found at i:1192950 original size:20 final size:18
Alignment explanation
Indices: 1192922--1192962 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
1192912 TAAATTATAA
1192922 ATATAATAATTTATATATTC
1 ATATAATAA-TTATATA-TC
*
1192942 ATATCATAATTATATATC
1 ATATAATAATTATATATC
1192960 ATA
1 ATA
1192963 ATTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 7 0.35
20 8 0.40
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATAATTATATATC
Found at i:1192960 original size:13 final size:13
Alignment explanation
Indices: 1192942--1192971 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1192932 TTATATATTC
1192942 ATATCATAATTAT
1 ATATCATAATTAT
1192955 ATATCATAATTAT
1 ATATCATAATTAT
1192968 ATAT
1 ATAT
1192972 TTTATTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATCATAATTAT
Found at i:1193062 original size:32 final size:32
Alignment explanation
Indices: 1192992--1193075 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
1192982 TATAATTATT
* *
1192992 TTTAAAATATT-TTATA-TT-T-TTATATAAA
1 TTTAAAATATTAATATATTTATATTAAATAAA
*
1193020 TTTAATATATTAATA-ATTTATATTAAATAAA
1 TTTAAAATATTAATATATTTATATTAAATAAA
*
1193051 TTTTAAAATATTCATATATTTATAT
1 -TTTAAAATATTAATATATTTATAT
1193076 CATATTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 11 0.24
29 4 0.09
30 1 0.02
31 8 0.18
32 13 0.29
33 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTAAAATATTAATATATTTATATTAAATAAA
Found at i:1198198 original size:20 final size:20
Alignment explanation
Indices: 1198170--1198207 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1198160 ATTTCACGTA
1198170 ATATAAAAAATAATATAAAT
1 ATATAAAAAATAATATAAAT
* *
1198190 ATATTAAAATTAATATAA
1 ATATAAAAAATAATATAA
1198208 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATAAAAAATAATATAAAT
Found at i:1198231 original size:17 final size:17
Alignment explanation
Indices: 1198198--1198242 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1198188 ATATATTAAA
*
1198198 ATTAATATAATTTAAATT
1 ATTAATA-AATTAAAATT
1198216 ATTAATAAATTAAAATT
1 ATTAATAAATTAAAATT
1198233 -TTATATAAAT
1 ATTA-ATAAAT
1198243 ATAATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.60
18 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAATAAATTAAAATT
Found at i:1198260 original size:32 final size:32
Alignment explanation
Indices: 1198183--1198262 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1198173 TAAAAAATAA
*
1198183 TATAAATATATTAAAATTAATATAATTTAAAT
1 TATAAATATATTAAAATTAATATAATATAAAT
* * *
1198215 TATTAATAAATTAAAATTTTATATAA-ATATAAT
1 TATAAATATATTAAAA-TTAATATAATATA-AAT
1198248 TA-AAATATATTAAAA
1 TATAAATATATTAAAA
1198263 AACTCATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 27 0.68
33 13 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TATAAATATATTAAAATTAATATAATATAAAT
Found at i:1198974 original size:25 final size:25
Alignment explanation
Indices: 1198924--1198976 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1198914 CGGTCTCATA
** *
1198924 TTATGTCATATTTTTATTACTTTAT
1 TTATGTCATATTCGTATTAATTTAT
1198949 TTATGTCATATTCGTA-TAATTGTAT
1 TTATGTCATATTCGTATTAATT-TAT
1198974 TTA
1 TTA
1198977 ATATTACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (25 bp):
TTATGTCATATTCGTATTAATTTAT
Found at i:1200093 original size:15 final size:15
Alignment explanation
Indices: 1200032--1200122 Score: 71
Period size: 15 Copynumber: 5.9 Consensus size: 15
1200022 AATATGTTTA
1200032 AAAATATATACAATAT
1 AAAATATATA-AATAT
* *
1200048 GAATTAT-TAATATAT
1 AAAATATATAA-ATAT
1200063 CAAAATAATATAAATAT
1 -AAAAT-ATATAAATAT
*
1200080 AAAATATTTAAATAT
1 AAAATATATAAATAT
* *
1200095 GATAATA-ATATA-AT
1 -AAAATATATAAATAT
1200109 AAAATATATAAATA
1 AAAATATATAAATA
1200123 CAATTTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
13 5 0.09
14 7 0.12
15 19 0.33
16 18 0.31
17 6 0.10
18 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATATATAAATAT
Found at i:1200101 original size:29 final size:29
Alignment explanation
Indices: 1200067--1200122 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1200057 ATATATCAAA
*
1200067 ATAATATAAAT-ATAAAATATTTAAATATG
1 ATAATA-AAATAATAAAATATATAAATATG
*
1200096 ATAATAATATAATAAAATATATAAATA
1 ATAATAAAATAATAAAATATATAAATA
1200123 CAATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
ATAATAAAATAATAAAATATATAAATATG
Found at i:1200121 original size:8 final size:8
Alignment explanation
Indices: 1200033--1200122 Score: 51
Period size: 8 Copynumber: 10.6 Consensus size: 8
1200023 ATATGTTTAA
1200033 AAATATAT
1 AAATATAT
*
1200041 ACA-ATAT
1 AAATATAT
*
1200048 GAAT-TAT
1 AAATATAT
*
1200055 TAATATAT
1 AAATATAT
1200063 CAAAATAATAT
1 --AAAT-ATAT
1200074 AAATATA-
1 AAATATAT
*
1200081 AAATATTT
1 AAATATAT
1200089 AAATATGAT
1 AAATAT-AT
1200098 AATAATATAAT
1 -A-AATAT-AT
1200109 AAAATATAT
1 -AAATATAT
1200118 AAATA
1 AAATA
1200123 CAATTTAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
7 17 0.26
8 19 0.29
9 7 0.11
10 9 0.14
11 13 0.20
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (8 bp):
AAATATAT
Found at i:1200469 original size:18 final size:18
Alignment explanation
Indices: 1200438--1200532 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 18
1200428 AAGTATAATA
1200438 ATATTTA-A-AATATTAT
1 ATATTTATATAATATTAT
1200454 ATATTTATATAATATT-T
1 ATATTTATATAATATTAT
*
1200471 A-ATATAT-TAATAATT-T
1 ATATTTATATAAT-ATTAT
*
1200487 ATA-TTATATTAATTTTAAT
1 ATATTTATA-TAATATT-AT
*
1200506 ATATTTAAAT-AT-TTAT
1 ATATTTATATAATATTAT
1200522 ATTATTT-TATA
1 A-TATTTATATA
1200533 TTACATCGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
15 4 0.06
16 25 0.40
17 13 0.21
18 12 0.19
19 5 0.08
20 4 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATATAATATTAT
Found at i:1200477 original size:27 final size:27
Alignment explanation
Indices: 1200435--1200512 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
1200425 TAAAAGTATA
*
1200435 ATAATATTTAAAATATTATATATTTAT
1 ATAATATTTAATATATTATATATTTAT
1200462 ATAATATTTAATATATTA-ATAATTTAT
1 ATAATATTTAATATATTATAT-ATTTAT
*
1200489 ATTATA-TTAAT-T-TTAATATATTTA
1 ATAATATTTAATATATT-ATATATTTA
1200513 AATATTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
24 2 0.04
25 7 0.15
26 9 0.20
27 28 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATAATATTTAATATATTATATATTTAT
Found at i:1200490 original size:15 final size:14
Alignment explanation
Indices: 1200412--1200509 Score: 60
Period size: 14 Copynumber: 6.7 Consensus size: 14
1200402 GTAAAACATT
1200412 TTTAATATA-AATA
1 TTTAATATATAATA
**
1200425 TAAAAGTATAATAATA
1 TTTAA-TAT-ATAATA
* *
1200441 TTTAAAATATTATA
1 TTTAATATATAATA
1200455 TATT--TATATAATA
1 T-TTAATATATAATA
1200468 TTTAATATATTAATAA
1 TTTAATATA-TAAT-A
1200484 TTTATATTATATTAAT-
1 TTTA-A-TATA-TAATA
1200500 TTTAATATAT
1 TTTAATATAT
1200510 TTAAATATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
12 2 0.03
13 12 0.18
14 17 0.25
15 10 0.15
16 16 0.24
17 1 0.01
18 9 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
TTTAATATATAATA
Found at i:1200513 original size:15 final size:15
Alignment explanation
Indices: 1200463--1200513 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1200453 TATATTTATA
1200463 TAATATTTAATATATT
1 TAAT-TTTAATATATT
*
1200479 AATAATTTATATTATA-T
1 --TAATTT-TAATATATT
1200496 TAATTTTAATATATT
1 TAATTTTAATATATT
1200511 TAA
1 TAA
1200514 ATATTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 6 0.21
15 10 0.34
17 3 0.10
18 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTTAATATATT
Found at i:1200517 original size:27 final size:26
Alignment explanation
Indices: 1200452--1200530 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 26
1200442 TTAAAATATT
*
1200452 ATATATTT-ATATAATATTTAATATATTA
1 ATATATTTAATATTATA-TTAAT-T-TTA
1200480 ATA-ATTT-ATATTATATTAATTTTA
1 ATATATTTAATATTATATTAATTTTA
1200504 ATATATTTAAATATTTATATT-ATTTTA
1 ATATATTT-AATA-TTATATTAATTTTA
1200531 TATTACATCG
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
24 6 0.13
25 5 0.11
26 5 0.11
27 20 0.43
28 10 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATATTTAATATTATATTAATTTTA
Found at i:1200520 original size:33 final size:35
Alignment explanation
Indices: 1200433--1200526 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 35
1200423 TATAAAAGTA
1200433 TAATAATATTTAAAATATTATATATT-TATATAATATT
1 TAAT-ATATTT-AAATATT-TATATTATATATAATATT
1200470 TAATATA-TT-AATAATTTATATTATAT-TAAT-TT
1 TAATATATTTAAAT-ATTTATATTATATATAATATT
1200502 TAATATATTTAAATATTTATATTAT
1 TAATATATTTAAATATTTATATTAT
1200527 TTTATATTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
32 9 0.17
33 26 0.49
34 9 0.17
35 2 0.04
36 3 0.06
37 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TAATATATTTAAATATTTATATTATATATAATATT
Found at i:1201653 original size:19 final size:17
Alignment explanation
Indices: 1201629--1201678 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1201619 TGATATTAAA
1201629 AAAATTATTAATTTAATAT
1 AAAATTATTAATTT--TAT
*
1201648 AAAATT-TTTATTTTAT
1 AAAATTATTAATTTTAT
*
1201664 AAAAATATTAATTTT
1 AAAATTATTAATTTT
1201679 TTGAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.30
17 7 0.26
18 6 0.22
19 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAATTATTAATTTTAT
Found at i:1201679 original size:18 final size:17
Alignment explanation
Indices: 1201628--1201678 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1201618 TTGATATTAA
*
1201628 AAAAATTATTAATTTAAT
1 AAAAA-TATTAATTTTAT
* *
1201646 ATAAAATTTTTATTTTAT
1 A-AAAATATTAATTTTAT
1201664 AAAAATATTAATTTT
1 AAAAATATTAATTTT
1201679 TTGAATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAAATATTAATTTTAT
Found at i:1202177 original size:15 final size:15
Alignment explanation
Indices: 1202157--1202214 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1202147 TAAAGTATTA
1202157 TTTAATTATATAAAT
1 TTTAATTATATAAAT
*
1202172 TTTAATTATATTAATAA
1 TTTAATTATA-TAA-AT
*
1202189 TTCATATTATATAAAT
1 TTTA-ATTATATAAAT
1202205 TTTAA-TATAT
1 TTTAATTATAT
1202215 TCATATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 5 0.14
15 11 0.31
16 7 0.19
17 7 0.19
18 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTATATAAAT
Found at i:1202181 original size:37 final size:34
Alignment explanation
Indices: 1202133--1202215 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 34
1202123 ATTTTTAAAT
*
1202133 ATTTTAATTATATTTAAAGTATTATTTA-ATTATATAA
1 ATTTTAATTATATTT-AA-TA--ATTCATATTATATAA
1202170 ATTTTAATTATA-TTAATAATTCATATTATATAA
1 ATTTTAATTATATTTAATAATTCATATTATATAA
1202203 ATTTTAA-TATATT
1 ATTTTAATTATATT
1202216 CATATATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
32 8 0.19
33 17 0.40
34 2 0.05
35 2 0.05
36 2 0.05
37 12 0.28
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
ATTTTAATTATATTTAATAATTCATATTATATAA
Found at i:1202203 original size:33 final size:33
Alignment explanation
Indices: 1202161--1202229 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1202151 GTATTATTTA
1202161 ATTATATAAATTTTAATTATATTAATA-ATTCAT
1 ATTATATAAATTTTAA-TATATTAATATATTCAT
* *
1202194 ATTATATAAATTTTAATATATTCATATATTTAT
1 ATTATATAAATTTTAATATATTAATATATTCAT
1202227 ATT
1 ATT
1202230 TATTTTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (33 bp):
ATTATATAAATTTTAATATATTAATATATTCAT
Found at i:1202227 original size:6 final size:6
Alignment explanation
Indices: 1202218--1202315 Score: 61
Period size: 6 Copynumber: 17.3 Consensus size: 6
1202208 AATATATTCA
* * * *
1202218 TATATT TATATT TAT-TT T-TGTT AATTTTT TATATAT TA-ATA TA-ATT
1 TATATT TATATT TATATT TATATT TA-TATT TATAT-T TATATT TATATT
*
1202264 TAT--T TATATT TATATT T-TAATT TAT-TT TTTATT TATATT TATA-T
1 TATATT TATATT TATATT TAT-ATT TATATT TATATT TATATT TATATT
1202308 TATATT TA
1 TATATT TA
1202316 AAATTATTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
4 5 0.07
5 21 0.29
6 39 0.53
7 8 0.11
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:1202273 original size:19 final size:20
Alignment explanation
Indices: 1202239--1202278 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1202229 TTATTTTTGT
*
1202239 TAATTTTTTATATATTAATA
1 TAATTTATTATATATTAATA
*
1202259 TAATTTATT-TATATTTATA
1 TAATTTATTATATATTAATA
1202278 T
1 T
1202279 TTTAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTATTATATATTAATA
Found at i:1202286 original size:12 final size:12
Alignment explanation
Indices: 1202266--1202303 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1202256 ATATAATTTA
1202266 TTTATATTTATAT
1 TTTA-ATTTATAT
1202279 TTTAATTTAT-T
1 TTTAATTTATAT
*
1202290 TTTTATTTATAT
1 TTTAATTTATAT
1202302 TT
1 TT
1202304 ATATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 9 0.39
13 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTAATTTATAT
Found at i:1202322 original size:17 final size:17
Alignment explanation
Indices: 1202265--1202322 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1202255 AATATAATTT
*
1202265 ATTTATATTTATATTTTA
1 ATTTATA-TTATATTTAA
* * *
1202283 ATTTATTTTTTATTTAT
1 ATTTATATTATATTTAA
1202300 ATTTATATTATATTTAA
1 ATTTATATTATATTTAA
*
1202317 AATTAT
1 ATTTAT
1202323 TATACCGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 26 0.81
18 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTATATTATATTTAA
Found at i:1202541 original size:21 final size:21
Alignment explanation
Indices: 1202503--1202567 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
1202493 GTTTTTAAAA
**
1202503 AATATTTTAATTAATATATAT
1 AATATTTTAATTTTTATATAT
1202524 AATATTTTAATTTTTATA-ATT
1 AATATTTTAATTTTTATATA-T
1202545 AA-ATTTTATTATTTTTAATATAT
1 AATATTTTA--ATTTTT-ATATAT
1202568 TCTATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 7 0.19
21 19 0.51
22 6 0.16
23 4 0.11
24 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATATTTTAATTTTTATATAT
Found at i:1202610 original size:21 final size:22
Alignment explanation
Indices: 1202586--1202635 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1202576 TTTAATTTAA
*
1202586 AAATATTTTTATTGTATT-TTT
1 AAATATTTTTATTGTATTAATT
* *
1202607 AAATA-TATTATTTTATTAATT
1 AAATATTTTTATTGTATTAATT
1202628 AAATATTT
1 AAATATTT
1202636 ATTTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.43
21 12 0.52
22 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
AAATATTTTTATTGTATTAATT
Found at i:1202641 original size:45 final size:46
Alignment explanation
Indices: 1202547--1202647 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 46
1202537 TTATAATTAA
*
1202547 ATTTTA-TTATTTTTAATATATTCTATTTTTTTAATTTAAAAATAT
1 ATTTTATTTATTTTTAATATATTCTATTTTATTAATTTAAAAATAT
* *
1202592 -TTTTATTGTATTTTTAA-ATATAT-TATTTTATTAA-TTAAATATTT
1 ATTTTATT-TATTTTTAATATAT-TCTATTTTATTAATTTAAAAATAT
1202636 ATTTTATATTAT
1 ATTTTAT-TTAT
1202648 AAAAAATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
44 13 0.27
45 24 0.50
46 11 0.23
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (46 bp):
ATTTTATTTATTTTTAATATATTCTATTTTATTAATTTAAAAATAT
Found at i:1202650 original size:20 final size:19
Alignment explanation
Indices: 1202570--1202650 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 19
1202560 TAATATATTC
*
1202570 TATTT-TTTTAATTTAAAAA
1 TATTTATTTT-ATTTATAAA
* *
1202589 TATTTTTATTGTATTTTTAAA
1 TA--TTTATTTTATTTATAAA
*
1202610 TATATTATTTTATTAATTAAA
1 TAT-TTATTTTATTTA-TAAA
1202631 TATTTATTTTATATTATAAA
1 TATTTATTTTAT-TTATAAA
1202651 AAATTAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
19 3 0.06
20 22 0.45
21 21 0.43
22 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTTATTTTATTTATAAA
Found at i:1202695 original size:27 final size:26
Alignment explanation
Indices: 1202665--1202716 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1202655 TAAAAATAAA
1202665 ATAA-AAATATAATTTAATTTAATTTAG
1 ATAATAAA-ATAATTT-ATTTAATTTAG
* *
1202692 ATAATAAAGTAATTTTTTTAATTTA
1 ATAATAAAATAATTTATTTAATTTA
1202717 AAATAAGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
ATAATAAAATAATTTATTTAATTTAG
Found at i:1204502 original size:2 final size:2
Alignment explanation
Indices: 1204495--1204520 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1204485 AATCAAATGG
1204495 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
1204521 TGAGGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1209464 original size:2 final size:2
Alignment explanation
Indices: 1209451--1209486 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1209441 AAAGGAAATG
*
1209451 AT AT AA 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
1209487 TTAGAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1211792 original size:12 final size:12
Alignment explanation
Indices: 1211775--1211799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1211765 GTATCGAACG
1211775 TCACAGAAACAA
1 TCACAGAAACAA
1211787 TCACAGAAACAA
1 TCACAGAAACAA
1211799 T
1 T
1211800 GATGCAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (12 bp):
TCACAGAAACAA
Found at i:1211834 original size:50 final size:51
Alignment explanation
Indices: 1211736--1211837 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 51
1211726 TGTTTTGCTG
* * *
1211736 TCACAGAGACAATGATGCAGGTAAGTCTGGTATCGAACGTCACAGAAACAA
1 TCACAGAAACAATGATGCAGATAAGTCTGGTAACGAACGTCACAGAAACAA
* * * * *
1211787 TCACAGAAACAATGATGCA-ATGAGTCTGGTAAGGCATGTCACGGAAACAA
1 TCACAGAAACAATGATGCAGATAAGTCTGGTAACGAACGTCACAGAAACAA
1211837 T
1 T
1211838 GCTGCAGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 25 0.58
51 18 0.42
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (51 bp):
TCACAGAAACAATGATGCAGATAAGTCTGGTAACGAACGTCACAGAAACAA
Found at i:1214006 original size:2 final size:2
Alignment explanation
Indices: 1214001--1214034 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1213991 GAGAGAGAGA
* *
1214001 GT GT GT GT GT GT GT GT GT GT TT GT GT CT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1214035 TTGGAATACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.44, T:0.53
Consensus pattern (2 bp):
GT
Found at i:1216957 original size:6 final size:6
Alignment explanation
Indices: 1216901--1216958 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
1216891 TTACAAATAA
*
1216901 TAAATT TAATATT TAAATT TATAATT TATAATT T--ATT TAAATC TAAA--
1 TAAATT TAA-ATT TAAATT TA-AATT TA-AATT TAAATT TAAATT TAAATT
1216948 TAAATT TAAAT
1 TAAATT TAAAT
1216959 AATATTATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
4 8 0.18
6 19 0.42
7 18 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:1217074 original size:22 final size:24
Alignment explanation
Indices: 1217049--1217106 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1217039 TTTATTTATC
1217049 ATAATA-ATATTTAAAATAT-TTA
1 ATAATATATATTTAAAATATATTA
**
1217071 ATAATTATATATTTTTAATATATTA
1 ATAA-TATATATTTAAAATATATTA
*
1217096 ATAATTTATAT
1 ATAATATATAT
1217107 AATATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.13
23 2 0.07
24 17 0.57
25 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAATATATATTTAAAATATATTA
Found at i:1217094 original size:26 final size:26
Alignment explanation
Indices: 1217058--1217107 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1217048 CATAATAATA
1217058 TTTAAAATATTTAATAA-TTATATATT
1 TTTAAAATA-TTAATAATTTATATATT
*
1217084 TTTAATATATTAATAATTTATATA
1 TTTAAAATATTAATAATTTATATA
1217108 ATATAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAAAATATTAATAATTTATATATT
Found at i:1217116 original size:26 final size:24
Alignment explanation
Indices: 1217062--1217118 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
1217052 ATAATATTTA
* *
1217062 AAATATTTAATAATTATATATTTT
1 AAATATTTAATAATTATATAATAT
*
1217086 TAATATATTAATAATTTATATAATAT
1 AAATAT-TTAATAA-TTATATAATAT
1217112 AAATATT
1 AAATATT
1217119 AAAATATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 5 0.19
25 8 0.30
26 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATATTTAATAATTATATAATAT
Found at i:1219630 original size:2 final size:2
Alignment explanation
Indices: 1219623--1219651 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1219613 ACGTGGACGA
1219623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1219652 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1219865 original size:22 final size:22
Alignment explanation
Indices: 1219815--1219909 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 22
1219805 TTAAGTTGAA
1219815 TTAAATTA-AATTTAAAATTAAT
1 TTAAATTATAATTT-AAATTAAT
** *
1219837 TT-TTTTATAATTTAATTTAAT
1 TTAAATTATAATTTAAATTAAT
* *
1219858 TTAATTTATTATTT--ATTAA-
1 TTAAATTATAATTTAAATTAAT
* *
1219877 TTAAATTATTATTTTAAATTAAA
1 TTAAATTA-TAATTTAAATTAAT
1219900 TT-AATTATAA
1 TTAAATTATAA
1219910 AATATATTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
19 7 0.12
20 8 0.14
21 14 0.25
22 26 0.46
23 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAATTATAATTTAAATTAAT
Found at i:1219885 original size:19 final size:18
Alignment explanation
Indices: 1219852--1219907 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1219842 TATAATTTAA
*
1219852 TTTAATTTAATTTATTATT
1 TTTAA-TTAAATTATTATT
1219871 TATTAATTAAATTATTATT
1 T-TTAATTAAATTATTATT
*
1219890 TTAAATTAAATTAATTAT
1 TTTAATTAAATT-ATTAT
1219908 AAAATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 10 0.30
19 19 0.58
20 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAATTAAATTATTATT
Found at i:1219942 original size:17 final size:21
Alignment explanation
Indices: 1219894--1219935 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1219884 ATTATTTTAA
*
1219894 ATTAAATTAATTATAAAATAT
1 ATTATATTAATTATAAAATAT
*
1219915 ATTATATTAATTAAAAAATAT
1 ATTATATTAATTATAAAATAT
1219936 TTTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTATATTAATTATAAAATAT
Found at i:1227631 original size:30 final size:30
Alignment explanation
Indices: 1227597--1227676 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
1227587 AGTGGTGCAT
1227597 TAGTCCTTAATTTAAGGGATAGTAGCGCAC
1 TAGTCCTTAATTTAAGGGATAGTAGCGCAC
* * *
1227627 TAGTCCTT-ATTCTAAGGAATAGTGGTGCAC
1 TAGTCCTTAATT-TAAGGGATAGTAGCGCAC
1227657 TAGTCCTTAATTTAAGGGAT
1 TAGTCCTTAATTTAAGGGAT
1227677 TTAAATTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.07
30 38 0.86
31 3 0.07
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (30 bp):
TAGTCCTTAATTTAAGGGATAGTAGCGCAC
Found at i:1227918 original size:32 final size:33
Alignment explanation
Indices: 1227863--1227927 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1227853 TTGAGAACCT
** *
1227863 AAATTTTTTTTTTCTGTTCAGCCTTCATTGCTG
1 AAATTTTTTTTTTCTAATCAGCCTTAATTGCTG
1227896 AAATTTTTTTTTTCTAAT-AGCCTTAATTGCTG
1 AAATTTTTTTTTTCTAATCAGCCTTAATTGCTG
1227928 GTTTTTGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (33 bp):
AAATTTTTTTTTTCTAATCAGCCTTAATTGCTG
Found at i:1232137 original size:30 final size:30
Alignment explanation
Indices: 1232049--1232140 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
1232039 TTTAAATTAA
* * *
1232049 ATAGTGGTACATTAGTCCTTAATTTAAGAG
1 ATAGTGGTGCACTAGTCCTTAATTTAAGGG
*
1232079 ATAGTGGTGCACTAGTCCTTAATCTAAGGG
1 ATAGTGGTGCACTAGTCCTTAATTTAAGGG
1232109 ATAGTAGG-GCACTAGTCCTTAATTTAAGGG
1 ATAGT-GGTGCACTAGTCCTTAATTTAAGGG
1232139 AT
1 AT
1232141 TTAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 54 0.96
31 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (30 bp):
ATAGTGGTGCACTAGTCCTTAATTTAAGGG
Found at i:1240053 original size:46 final size:46
Alignment explanation
Indices: 1239991--1240083 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
1239981 TATGTAAAAT
1239991 CAACTACAATCAATATTACTCATTTAATATGTGAATTAAAAACTTA
1 CAACTACAATCAATATTACTCATTTAATATGTGAATTAAAAACTTA
*
1240037 CAACTACAATCCATATTACTCATTTAATATGTGAATTAAAAACTTA
1 CAACTACAATCAATATTACTCATTTAATATGTGAATTAAAAACTTA
1240083 C
1 C
1240084 TTTCCCAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.34
Consensus pattern (46 bp):
CAACTACAATCAATATTACTCATTTAATATGTGAATTAAAAACTTA
Found at i:1240560 original size:17 final size:17
Alignment explanation
Indices: 1240535--1240579 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1240525 GATTACAAAT
1240535 CATGAGTGATAAAATCAC
1 CATG-GTGATAAAATCAC
* * *
1240553 CTTGGTGATTAAATTAC
1 CATGGTGATAAAATCAC
1240570 CATGGTGATA
1 CATGGTGATA
1240580 TTAAAAATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (17 bp):
CATGGTGATAAAATCAC
Found at i:1241503 original size:63 final size:64
Alignment explanation
Indices: 1241398--1241517 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 64
1241388 GAATAACCCA
* *
1241398 CCATGTTCTTGTAGATATGGAAAAAAAATCTAACTGTGATCTGACAAGCAATGACGTGAGCCTG
1 CCATGTTCTTGTAGACATGGAAAAAAAATCTAACTGTAATCTGACAAGCAATGACGTGAGCCTG
* * *
1241462 CCATGTTCTTTTAGACATGG-AAAAAAATCTAACTGTAATCTGACATGCAGTGACGT
1 CCATGTTCTTGTAGACATGGAAAAAAAATCTAACTGTAATCTGACAAGCAATGACGT
1241518 AATTTGATAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 33 0.65
64 18 0.35
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (64 bp):
CCATGTTCTTGTAGACATGGAAAAAAAATCTAACTGTAATCTGACAAGCAATGACGTGAGCCTG
Found at i:1244509 original size:17 final size:17
Alignment explanation
Indices: 1244471--1244525 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1244461 CTAAATTTTT
* *
1244471 AAAA-TTAATTATTTAT
1 AAAATTTAAATATTTAA
* *
1244487 AGAATTTAAATTTTTAA
1 AAAATTTAAATATTTAA
*
1244504 CAAATTTAAATATTTAA
1 AAAATTTAAATATTTAA
1244521 AAAAT
1 AAAAT
1244526 AATATTTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 3 0.10
17 27 0.90
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AAAATTTAAATATTTAA
Found at i:1244556 original size:26 final size:27
Alignment explanation
Indices: 1244505--1244565 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
1244495 AATTTTTAAC
*
1244505 AAATTTAAATATTTAAAAAATAATATTT
1 AAATTT-AATATTTAAAAAATAATATAT
* * *
1244533 TAATTTAA-ATTTAAAAATTTATATAT
1 AAATTTAATATTTAAAAAATAATATAT
1244559 AAATTTA
1 AAATTTA
1244566 TACAAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 21 0.75
27 2 0.07
28 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTTAATATTTAAAAAATAATATAT
Found at i:1244872 original size:28 final size:30
Alignment explanation
Indices: 1244815--1244872 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
1244805 TAAGTAAATA
*
1244815 TTAATTATAAAAATATTATCTAAATTTAAT
1 TTAATTATAAAAATATTATCTAAATATAAT
*
1244845 TTAATTA-AAATAAT-TTAT-TAACTATAAT
1 TTAATTATAAA-AATATTATCTAAATATAAT
1244873 ATTTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.32
29 7 0.28
30 10 0.40
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAATTATAAAAATATTATCTAAATATAAT
Found at i:1244890 original size:17 final size:17
Alignment explanation
Indices: 1244845--1244893 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1244835 TAAATTTAAT
1244845 TTAATTAAAATAATTTA
1 TTAATTAAAATAATTTA
* * *
1244862 TTAACTATAAT-ATTTT
1 TTAATTAAAATAATTTA
1244878 TATAATTAAAATAATT
1 T-TAATTAAAATAATT
1244894 ATAAATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.20
17 17 0.68
18 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATTAAAATAATTTA
Found at i:1244929 original size:27 final size:27
Alignment explanation
Indices: 1244899--1244954 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1244889 TAATTATAAA
1244899 TATT-AATTATAAAAAATAAATTAAATT
1 TATTAAATTA-AAAAAATAAATTAAATT
* * *
1244926 TATTAAATTAAATAAATAATTTAATTT
1 TATTAAATTAAAAAAATAAATTAAATT
1244953 TA
1 TA
1244955 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTAAATTAAAAAAATAAATTAAATT
Found at i:1245567 original size:9 final size:9
Alignment explanation
Indices: 1245553--1245578 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1245543 ACTGCTACTT
1245553 CCACTGCTA
1 CCACTGCTA
1245562 CCACTGCTA
1 CCACTGCTA
1245571 CCACTGCT
1 CCACTGCT
1245579 TCTTCTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.46, G:0.12, T:0.23
Consensus pattern (9 bp):
CCACTGCTA
Found at i:1246859 original size:99 final size:100
Alignment explanation
Indices: 1246688--1246888 Score: 359
Period size: 99 Copynumber: 2.0 Consensus size: 100
1246678 ACTGAAATTT
1246688 TAGGTTTGGATTGAAATAAAGTTGCACATTAATATCATCTATCACGGGGATCAAAGATGTTGGGA
1 TAGGTTTGGATTGAAATAAAGTTGCACATTAATATCATCTATCACGGGGATCAAAGATGTTGGGA
1246753 TGC-TTTTTTTTTTCGGATAATTAATGTTGGGATG
66 TGCTTTTTTTTTTTCGGATAATTAATGTTGGGATG
*
1246787 TAGGTTTGGATTGTAATAAAGTTGCACATTAATATCATCTATCACGGGGATCAAAGATGTTGGGA
1 TAGGTTTGGATTGAAATAAAGTTGCACATTAATATCATCTATCACGGGGATCAAAGATGTTGGGA
*
1246852 TGCTTTTTTTTTTTTTTGGATAATTAATGTTGGGATG
66 TGC--TTTTTTTTTTTCGGATAATTAATGTTGGGATG
1246889 CTTTTTAGTT
Statistics
Matches: 97, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
99 67 0.69
102 30 0.31
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.40
Consensus pattern (100 bp):
TAGGTTTGGATTGAAATAAAGTTGCACATTAATATCATCTATCACGGGGATCAAAGATGTTGGGA
TGCTTTTTTTTTTTCGGATAATTAATGTTGGGATG
Found at i:1264518 original size:16 final size:16
Alignment explanation
Indices: 1264442--1264531 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 16
1264432 GCATTTTATG
*
1264442 TATTTTATTTTTATAT
1 TATTTTATATTTATAT
* *
1264458 TAATTTGATATTT-TAA
1 T-ATTTTATATTTATAT
* *
1264474 TAATTCATA-TTATAT
1 TATTTTATATTTATAT
* *
1264489 AAATTTTAAAATTTATAT
1 -TATTTT-ATATTTATAT
* *
1264507 TTTTTTATATTTTTAT
1 TATTTTATATTTATAT
1264523 TATTTTATA
1 TATTTTATA
1264532 CATGTCAAAC
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
14 2 0.04
15 8 0.15
16 23 0.43
17 15 0.28
18 6 0.11
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
TATTTTATATTTATAT
Found at i:1266006 original size:24 final size:28
Alignment explanation
Indices: 1265960--1266022 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
1265950 TTTCGTATTG
*
1265960 ATATTTATATTTTAATAATA-TTTTTT-
1 ATATTTATATATTAATAATATTTTTTTA
1265986 ATATTTATA-ATT-ATAATATTTTTTTA
1 ATATTTATATATTAATAATATTTTTTTA
1266012 ATATTTATATA
1 ATATTTATATA
1266023 CAAAACTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 6 0.18
25 8 0.24
26 18 0.55
27 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTTATATATTAATAATATTTTTTTA
Found at i:1275718 original size:22 final size:21
Alignment explanation
Indices: 1275673--1275741 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
1275663 TATATGATAC
* * *
1275673 AAATATAACATTAAAAAAATTA
1 AAATATAATA-TAAATATATTA
1275695 AAATATAATAT-AATATAATATA
1 AAATATAATATAAATAT-AT-TA
*
1275717 AAAAATAATATAAATATATTA
1 AAATATAATATAAATATATTA
1275738 AAAT
1 AAAT
1275742 TAAAAACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.08
21 8 0.21
22 23 0.59
23 5 0.13
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATATAATATAAATATATTA
Found at i:1275726 original size:27 final size:27
Alignment explanation
Indices: 1275677--1275747 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
1275667 TGATACAAAT
* *
1275677 ATAACATTAAAAAAATTAAAATATAATATA
1 ATAAAATT-AAAAAA-TAATATA-AATATA
*
1275707 ATATAATATAAAAAATAATATAAATATA
1 ATAAAAT-TAAAAAATAATATAAATATA
*
1275735 TTAAAATTAAAAA
1 ATAAAATTAAAAA
1275748 CATATCACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 6 0.17
28 11 0.31
29 6 0.17
30 11 0.31
31 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (27 bp):
ATAAAATTAAAAAATAATATAAATATA
Found at i:1276580 original size:19 final size:19
Alignment explanation
Indices: 1276535--1276628 Score: 67
Period size: 19 Copynumber: 5.1 Consensus size: 19
1276525 ATCTTTTTTA
*
1276535 TATATATATATTATAAATT
1 TATATATTTATTATAAATT
*
1276554 TA-ATTATTTATTTTAAATT
1 TATA-TATTTATTATAAATT
1276573 TATATATTTTATTAT--A-T
1 TATATA-TTTATTATAAATT
1276590 TATA-ATTTTACTTA-AAATAT
1 TATATA-TTTA-TTATAAAT-T
*
1276610 TTTATATTTA-TATAAATT
1 TATATATTTATTATAAATT
1276628 T
1 T
1276629 TAATATCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
16 6 0.10
17 8 0.13
18 7 0.11
19 23 0.38
20 16 0.26
21 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATATTTATTATAAATT
Found at i:1276647 original size:22 final size:22
Alignment explanation
Indices: 1276621--1276662 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1276611 TTATATTTAT
*
1276621 ATAAATTTTAATATCATATTAA
1 ATAAATTTTAAAATCATATTAA
*
1276643 ATAAATTTTAAAATTATATT
1 ATAAATTTTAAAATCATATT
1276663 TATATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTTTAAAATCATATTAA
Found at i:1276832 original size:13 final size:13
Alignment explanation
Indices: 1276814--1276857 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1276804 TATTTTTTTA
1276814 AATATTTATATTT
1 AATATTTATATTT
*
1276827 AATATTTATGTTT
1 AATATTTATATTT
1276840 AATA--TATATTT
1 AATATTTATATTT
1276851 AA-ATTTA
1 AATATTTA
1276858 AATATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
12 2 0.07
13 16 0.59
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1276869 original size:23 final size:23
Alignment explanation
Indices: 1276820--1276897 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
1276810 TTTAAATATT
** * *
1276820 TATATTTAATATTTATGTTTAATA
1 TATATTTAA-ATTTAAATATAAAA
1276844 TATATTTAAATTTAAATATAAAA
1 TATATTTAAATTTAAATATAAAA
*
1276867 TATAATT--ATTTAAATATATAAA
1 TATATTTAAATTTAAATATA-AAA
*
1276889 -AAATTTAAA
1 TATATTTAAA
1276898 AATATTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 15 0.34
22 3 0.07
23 17 0.39
24 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (23 bp):
TATATTTAAATTTAAATATAAAA
Found at i:1276896 original size:17 final size:17
Alignment explanation
Indices: 1276851--1276914 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
1276841 ATATATATTT
*
1276851 AAATTTAAATATAAAATA
1 AAATTTAAATATATAA-A
1276869 TAATTATTTAAATATATAAA
1 -AA--ATTTAAATATATAAA
* *
1276889 AAATTTAAAAATATTAA
1 AAATTTAAATATATAAA
1276906 AAATATTAA
1 AAAT-TTAA
1276915 TATTTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 17 0.44
18 4 0.10
19 4 0.10
20 1 0.03
21 13 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAATATATAAA
Found at i:1276924 original size:19 final size:21
Alignment explanation
Indices: 1276902--1276944 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
1276892 TTTAAAAATA
*
1276902 TTAAAAATAT-TAAT-ATTTT
1 TTAAAAATATAAAATAATTTT
*
1276921 TTAAATATATAAAATAATTTT
1 TTAAAAATATAAAATAATTTT
1276942 TTA
1 TTA
1276945 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAAATATAAAATAATTTT
Found at i:1276956 original size:24 final size:23
Alignment explanation
Indices: 1276912--1276957 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1276902 TTAAAAATAT
*
1276912 TAATATTTTTTAAATATATAAAA
1 TAATATTTTTTAAATAAATAAAA
*
1276935 TAATTTTTTATTAAATAAATAAA
1 TAATATTTT-TTAAATAAATAAA
1276958 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTTTTTAAATAAATAAAA
Found at i:1277009 original size:20 final size:22
Alignment explanation
Indices: 1276981--1277049 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 22
1276971 ATTTTATCTC
1276981 AAATTAAATTTAAATT-TAAA-
1 AAATTAAATTTAAATTATAAAT
*
1277001 AAATAAAATTT-AATTATAAAT
1 AAATTAAATTTAAATTATAAAT
1277022 AAATTAAATTATAAATTA-AATAT
1 AAATTAAATT-TAAATTATAA-AT
1277045 AAATT
1 AAATT
1277050 TAAACTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.10
20 14 0.33
21 9 0.21
22 3 0.07
23 12 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTAAATTTAAATTATAAAT
Found at i:1277031 original size:16 final size:16
Alignment explanation
Indices: 1277001--1277053 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
1276991 TAAATTTAAA
*
1277001 AAATAAAATTTAATTAT
1 AAAT-AAATTAAATTAT
1277018 AAATAAATTAAATTAT
1 AAATAAATTAAATTAT
1277034 AAATTAAATATAAATT-T
1 AAA-TAAAT-TAAATTAT
1277051 AAA
1 AAA
1277054 CTTTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 14 0.42
17 13 0.39
18 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAAATTAAATTAT
Found at i:1277035 original size:12 final size:11
Alignment explanation
Indices: 1276981--1277049 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
1276971 ATTTTATCTC
*
1276981 AAATTAAATTT
1 AAATTAAATAT
*
1276992 AAATTTAA-A-
1 AAATTAAATAT
*
1277001 AAATAAAAT-T
1 AAATTAAATAT
*
1277011 TAATTATAA-AT
1 AAATTA-AATAT
1277022 AAATTAAATTAT
1 AAATTAAA-TAT
1277034 AAATTAAATAT
1 AAATTAAATAT
1277045 AAATT
1 AAATT
1277050 TAAACTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.13
10 6 0.13
11 23 0.51
12 10 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAAATAT
Found at i:1277052 original size:12 final size:12
Alignment explanation
Indices: 1276984--1277053 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 12
1276974 TTATCTCAAA
*
1276984 TTAAATTTAAAT
1 TTAAATATAAAT
*
1276996 TTAAAAAATAAAAT
1 TT-AAATAT-AAAT
*
1277010 TTAATTATAAAT
1 TTAAATATAAAT
1277022 AAATTAAATTATAAA-
1 ---TTAAA-TATAAAT
1277037 TTAAATATAAAT
1 TTAAATATAAAT
1277049 TTAAA
1 TTAAA
1277054 CTTTTTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
11 6 0.13
12 16 0.35
13 8 0.17
14 6 0.13
15 4 0.09
16 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAAATATAAAT
Found at i:1277548 original size:31 final size:31
Alignment explanation
Indices: 1277500--1277558 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1277490 ATTATTTTAA
* *
1277500 AATAAAAATATTATTTATTTATAAAAATATT
1 AATAAAAATATTATTTATTAAAAAAAATATT
1277531 AATAAAAA-ATTATTTTATTAAAAAAAAT
1 AATAAAAATATTA-TTTATTAAAAAAAAT
1277559 CTGAGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AATAAAAATATTATTTATTAAAAAAAATATT
Found at i:1281653 original size:81 final size:78
Alignment explanation
Indices: 1281518--1281670 Score: 173
Period size: 81 Copynumber: 1.9 Consensus size: 78
1281508 CGTGAAAAAA
* * * * ** * *
1281518 AAACTTAAAAAAATAAAAGATACCATGTCGGATTCATAACTGTATCTGCCACTCACGTTCAAGTT
1 AAACTTAAAAAAATAAAACACACCATGTCAGATTCATAACGGTATCTGAAACTCACATCCAAG-T
1281583 CAAGTAACAAGTAAC
65 -AAGTAACAAGTAAC
* *
1281598 AAACTTAGAAAAAATAAAACACCCCTTGTCAGATTCAT-ACAGGTATCTGAAACTCACATCCAAG
1 AAACTTA-AAAAAATAAAACACACCATGTCAGATTCATAAC-GGTATCTGAAACTCACATCCAAG
1281662 TAAGTAACA
64 TAAGTAACA
1281671 CAGATTAACT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
79 8 0.13
80 10 0.16
81 43 0.70
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (78 bp):
AAACTTAAAAAAATAAAACACACCATGTCAGATTCATAACGGTATCTGAAACTCACATCCAAGTA
AGTAACAAGTAAC
Found at i:1281882 original size:2 final size:2
Alignment explanation
Indices: 1281875--1281943 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1281865 AGCAAACAAA
1281875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1281917 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1281944 CCAAATTCAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1282444 original size:19 final size:19
Alignment explanation
Indices: 1282407--1282445 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1282397 TTTATTTAAT
1282407 TATTTATTAATTAAAATAA
1 TATTTATTAATTAAAATAA
*
1282426 TATTT-TTATTTAAATATAA
1 TATTTATTAATTAAA-ATAA
1282445 T
1 T
1282446 TATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTATTAATTAAAATAA
Found at i:1283210 original size:22 final size:24
Alignment explanation
Indices: 1283155--1283224 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
1283145 TTTACATATC
1283155 AAAAATATAT-TATTAAATTTAAT
1 AAAAATATATATATTAAATTTAAT
*
1283178 AATTAAT-TATAT-TTAAATTT-AT
1 AA-AAATATATATATTAAATTTAAT
* *
1283200 AAAAATATATAAAATTAAAATTAAT
1 AAAAATATAT-ATATTAAATTTAAT
1283225 TTTTATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 3 0.08
22 7 0.19
23 14 0.38
24 11 0.30
25 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATATATATATTAAATTTAAT
Found at i:1287497 original size:22 final size:22
Alignment explanation
Indices: 1287472--1287516 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1287462 AATATCACAT
1287472 TATAAAATAACAACATGATTGA
1 TATAAAATAACAACATGATTGA
** *
1287494 TATAAAATCCCAATATGATTGA
1 TATAAAATAACAACATGATTGA
1287516 T
1 T
1287517 GTAGCCTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (22 bp):
TATAAAATAACAACATGATTGA
Found at i:1287628 original size:2 final size:2
Alignment explanation
Indices: 1287621--1287650 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1287611 GATTAAGGTT
1287621 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
1287651 AAGGTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1287957 original size:20 final size:20
Alignment explanation
Indices: 1287930--1287986 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1287920 TTTAATTACA
1287930 AATTTATATTTTATAA-TAT
1 AATTTATATTTTATAACTAT
1287949 AATTATATATTTTATAACTAT
1 AATT-TATATTTTATAACTAT
1287970 AATAGTTATAATTTTAT
1 AAT--TTAT-ATTTTAT
1287987 TATATTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 6 0.18
22 3 0.09
23 8 0.24
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTTATATTTTATAACTAT
Found at i:1288918 original size:14 final size:15
Alignment explanation
Indices: 1288901--1288933 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1288891 CTTTTAAAAA
*
1288901 TACTTT-TTTTTCTT
1 TACTTTCTTTTCCTT
1288915 TACTTTCTTTTCCTT
1 TACTTTCTTTTCCTT
1288930 TACT
1 TACT
1288934 AATATCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (15 bp):
TACTTTCTTTTCCTT
Found at i:1292166 original size:48 final size:48
Alignment explanation
Indices: 1292074--1292195 Score: 192
Period size: 48 Copynumber: 2.6 Consensus size: 48
1292064 ATTATTCATT
1292074 TTTAAAGGTGGAATTTGTTGA-TTTTTTTTTTTACTAAGATGTTAGTA
1 TTTAAAGGTGGAATTTGTTGATTTTTTTTTTTTACTAAGATGTTAGTA
*
1292121 TTTGAAGGTGGAATTTGTTGATTTTTTTTTTTTACTAAGATGTTAGTA
1 TTTAAAGGTGGAATTTGTTGATTTTTTTTTTTTACTAAGATGTTAGTA
* * * *
1292169 TTTAAAGATGAAATTTGCTGATATTTT
1 TTTAAAGGTGGAATTTGTTGATTTTTT
1292196 ATTAAGGTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 20 0.29
48 48 0.71
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.52
Consensus pattern (48 bp):
TTTAAAGGTGGAATTTGTTGATTTTTTTTTTTTACTAAGATGTTAGTA
Found at i:1292793 original size:25 final size:24
Alignment explanation
Indices: 1292754--1292805 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
1292744 AAATGATTTG
* *
1292754 ATTTTAATCTTAAATTAAATTTAA
1 ATTTTAAACTTAAATCAAATTTAA
1292778 ATTTTAAAACTTAAATCAAATTTAA
1 ATTTT-AAACTTAAATCAAATTTAA
1292803 ATT
1 ATT
1292806 GCAATGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTTAAACTTAAATCAAATTTAA
Found at i:1292913 original size:3 final size:3
Alignment explanation
Indices: 1292905--1292944 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1292895 AAACCACTAA
1292905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1292945 TTTTGAGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1294210 original size:16 final size:16
Alignment explanation
Indices: 1294183--1294232 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1294173 TTATAATTAC
1294183 ATTTAAA-T-AATAAT
1 ATTTAAATTAAATAAT
**
1294197 ATTTTTATTAAATAAT
1 ATTTAAATTAAATAAT
1294213 AATTTAAATTAAATCAAT
1 -ATTTAAATTAAAT-AAT
1294231 AT
1 AT
1294233 AAATTAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 5 0.18
15 1 0.04
16 6 0.21
17 13 0.46
18 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAAATTAAATAAT
Found at i:1294873 original size:9 final size:10
Alignment explanation
Indices: 1294837--1294874 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1294827 ATTTTTTTTA
*
1294837 AATTTAATTT
1 AATTAAATTT
1294847 AATATAAATTT
1 AAT-TAAATTT
1294858 AATTAAATTT
1 AATTAAATTT
1294868 -ATTAAAT
1 AATTAAAT
1294875 CGGACGGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 7 0.27
10 10 0.38
11 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTAAATTT
Found at i:1295124 original size:3 final size:3
Alignment explanation
Indices: 1295109--1295147 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1295099 TTTCAATTTC
* *
1295109 CTT CTT TTT CTT CTT CTT GTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1295148 TATCGTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (3 bp):
CTT
Done.