Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 19
Found at i:1206145 original size:20 final size:20
Alignment explanation
Indices: 1206092--1206145 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
1206082 TAATTAAATT
1206092 TAAATTTTATTATAT-TTATA
1 TAAA-TTTATTATATATTATA
*
1206112 TAAATTT-TGATATATTA-A
1 TAAATTTATTATATATTATA
1206130 TAAATTATATTATATA
1 TAAATT-TATTATATA
1206146 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 12 0.41
19 7 0.24
20 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAAATTTATTATATATTATA
Found at i:1206170 original size:33 final size:30
Alignment explanation
Indices: 1206099--1206177 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 30
1206089 ATTTAAATTT
*
1206099 TATTATATTTATATAAATTTTGATATATTAA
1 TATTATA-TTATATAAATTTTAATATATTAA
1206130 TAAATTATATTATATAAATTTTAAAATATATTTAA
1 T--ATTATATTATATAAATTTT--AATATA-TTAA
1206165 TATTATATTATAT
1 TATTATATTATAT
1206178 TTTATAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 1 0.02
32 13 0.31
33 18 0.43
34 5 0.12
35 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TATTATATTATATAAATTTTAATATATTAA
Found at i:1206175 original size:38 final size:37
Alignment explanation
Indices: 1206089--1206189 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 37
1206079 TTATAATTAA
* *
1206089 ATTTAA-ATTTTATTATATTTATATAAATTTT-GATAT
1 ATTTAATATTATATTATA-TTATATAAATTTTAAATAT
1206125 A-TTAATA--A-ATTATATTATATAAATTTTAAAATAT
1 ATTTAATATTATATTATATTATATAAATTTT-AAATAT
*
1206159 ATTTAATATTATATTATATTTTAT-AATTTTA
1 ATTTAATATTATATTATATTATATAAATTTTA
1206190 TACGTATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
32 13 0.24
33 6 0.11
34 5 0.09
35 10 0.18
36 3 0.05
37 7 0.13
38 11 0.20
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
ATTTAATATTATATTATATTATATAAATTTTAAATAT
Found at i:1206190 original size:20 final size:20
Alignment explanation
Indices: 1206050--1206191 Score: 68
Period size: 19 Copynumber: 7.3 Consensus size: 20
1206040 GTTTTTAACA
1206050 TTTATATTATA-TTTATAAT
1 TTTATATTATATTTTATAAT
*
1206069 TTT-TATT-T-TATTATAAT
1 TTTATATTATATTTTATAAT
** * *
1206086 TAAAT-TTAAATTTTATTAT
1 TTTATATTATATTTTATAAT
*
1206105 ATTTATA-TAAATTTTGATATAT
1 -TTTATATTATATTTT-ATA-AT
* * *
1206127 TAATAAATTATATTATATAAAT
1 T-TTATATTATATTTTAT-AAT
* *
1206149 TTTA-A-AATATATT-TAAT
1 TTTATATTATATTTTATAAT
*
1206166 ATTATATTATATTTTATAAT
1 TTTATATTATATTTTATAAT
1206186 TTTATA
1 TTTATA
1206192 CGTATTTTAT
Statistics
Matches: 88, Mismatches: 21, Indels: 27
0.65 0.15 0.20
Matches are distributed among these distances:
17 17 0.19
18 7 0.08
19 21 0.24
20 21 0.24
21 5 0.06
22 10 0.11
23 7 0.08
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTATATTATATTTTATAAT
Found at i:1206362 original size:16 final size:16
Alignment explanation
Indices: 1206319--1206377 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1206309 TTTAATTGAT
*
1206319 ATTTAAAAAAATTTAA
1 ATTTAAAAAAAATTAA
*
1206335 A--T-AAAAATATTAA
1 ATTTAAAAAAAATTAA
1206348 ATTTAAAAAAAATTAA
1 ATTTAAAAAAAATTAA
*
1206364 ATCTAAAAATAAAT
1 ATTTAAAAA-AAAT
1206378 CTCGTTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 10 0.29
14 1 0.03
15 1 0.03
16 19 0.54
17 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTTAAAAAAAATTAA
Found at i:1206508 original size:21 final size:20
Alignment explanation
Indices: 1206473--1206544 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
1206463 ATTTTATTTT
1206473 TATA-ATATAAA-ATTAAAAA
1 TATATATATAAATATT-AAAA
* *
1206492 TATATATATAAATATTATAT
1 TATATATATAAATATTAAAA
*
1206512 TATAAACTATAAATATTAAAA
1 TATATA-TATAAATATTAAAA
*
1206533 TTTATAT-TAAAT
1 TATATATATAAAT
1206545 TATTTATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 9 0.21
20 15 0.35
21 19 0.44
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATATATAAATATTAAAA
Found at i:1206539 original size:41 final size:41
Alignment explanation
Indices: 1206465--1206564 Score: 116
Period size: 41 Copynumber: 2.4 Consensus size: 41
1206455 ATTTATATAT
* *
1206465 TTTATTTTTATAATATAAAATTAAAAATATATATATAAA-TA
1 TTTATATTTAAAATATAAAATTAAAAATATATAT-TAAATTA
* *
1206506 -TTATATTATAAACTATAAATATT-AAAATTTATATTAAATTA
1 TTTATATT-TAAAATATAAA-ATTAAAAATATATATTAAATTA
1206547 TTTATATTTAAAATATAA
1 TTTATATTTAAAATATAA
1206565 TAAAACATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
40 10 0.20
41 30 0.60
42 10 0.20
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (41 bp):
TTTATATTTAAAATATAAAATTAAAAATATATATTAAATTA
Found at i:1206594 original size:28 final size:25
Alignment explanation
Indices: 1206554--1206617 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 25
1206544 TTATTTATAT
1206554 TTAAAA-TATAATAAAACATATATAATTA
1 TTAAAATTA-AATAAAA-ATA-AT-ATTA
* *
1206582 TTAAAATTAAATAAAAATAATTTTT
1 TTAAAATTAAATAAAAATAATATTA
1206607 TTAAAATTAAA
1 TTAAAATTAAA
1206618 AATTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 13 0.39
26 2 0.06
27 3 0.09
28 13 0.39
29 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TTAAAATTAAATAAAAATAATATTA
Found at i:1206651 original size:10 final size:10
Alignment explanation
Indices: 1206638--1206671 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1206628 TATTTATTTT
1206638 TAAATATAAA
1 TAAATATAAA
*
1206648 TAAATATTAA
1 TAAATATAAA
*
1206658 TAAATTTAAA
1 TAAATATAAA
1206668 TAAA
1 TAAA
1206672 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAATATAAA
Found at i:1207270 original size:17 final size:17
Alignment explanation
Indices: 1207226--1207274 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1207216 TGTTAAATTG
1207226 TATATAAAAAATAATAA
1 TATATAAAAAATAATAA
*
1207243 T-T-TAAGTAAAATTATAA
1 TATATAA--AAAATAATAA
1207260 TATATAAAAAA-AATA
1 TATATAAAAAATAATA
1207275 TGTATACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
15 3 0.12
16 4 0.15
17 15 0.58
18 1 0.04
19 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TATATAAAAAATAATAA
Found at i:1208653 original size:13 final size:14
Alignment explanation
Indices: 1208637--1208666 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1208627 ATATTTTTAT
1208637 AATA-TTAAATTAA
1 AATACTTAAATTAA
1208650 AATACTTAAATTAA
1 AATACTTAAATTAA
1208664 AAT
1 AAT
1208667 TTTTGATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AATACTTAAATTAA
Found at i:1209212 original size:14 final size:14
Alignment explanation
Indices: 1209193--1209220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1209183 TTTTTTAATT
1209193 TTAAATATATTTTA
1 TTAAATATATTTTA
1209207 TTAAATATATTTTA
1 TTAAATATATTTTA
1209221 AATATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:1209229 original size:12 final size:12
Alignment explanation
Indices: 1209190--1209238 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
1209180 TATTTTTTTA
1209190 ATTTTAAATATAT
1 ATTTTAAATAT-T
*
1209203 TTTATTAAATA-T
1 ATT-TTAAATATT
1209215 ATTTTAAATATT
1 ATTTTAAATATT
*
1209227 ATTTTAATTATT
1 ATTTTAAATATT
1209239 TTAATTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 7 0.23
12 15 0.48
13 2 0.06
14 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTAAATATT
Found at i:1209299 original size:17 final size:17
Alignment explanation
Indices: 1209279--1209371 Score: 65
Period size: 17 Copynumber: 5.8 Consensus size: 17
1209269 GTCTAATTAA
1209279 TTAATTAAATTAATATT
1 TTAATTAAATTAATATT
* * *
1209296 TTAAATCAATTAAAATT
1 TTAATTAAATTAATATT
* **
1209313 TAAATTAAATTAATCAAA
1 TTAATTAAATTAAT-ATT
*
1209331 TTAATT-AATTAA-AAT
1 TTAATTAAATTAATATT
1209346 TTAA-T-AATT--T-TT
1 TTAATTAAATTAATATT
1209358 TTAATTAAATTAAT
1 TTAATTAAATTAAT
1209372 TTTAATCAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
12 5 0.09
13 1 0.02
14 9 0.16
15 6 0.10
16 1 0.02
17 30 0.52
18 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTAAATTAATATT
Found at i:1209320 original size:34 final size:34
Alignment explanation
Indices: 1209281--1209349 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1209271 CTAATTAATT
**
1209281 AATTAAATTAAT-ATTTTAAATCAATTAAAATTTA
1 AATTAAATTAATCAAATT-AATCAATTAAAATTTA
*
1209315 AATTAAATTAATCAAATTAATTAATTAAAATTTA
1 AATTAAATTAATCAAATTAATCAATTAAAATTTA
1209349 A
1 A
1209350 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 28 0.90
35 3 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (34 bp):
AATTAAATTAATCAAATTAATCAATTAAAATTTA
Found at i:1209361 original size:27 final size:28
Alignment explanation
Indices: 1209331--1209384 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1209321 ATTAATCAAA
1209331 TTAATT-AATTAAAATTTAAT-AATTTTT
1 TTAATTAAATT-AAATTTAATCAATTTTT
*
1209358 TTAATTAAATTAATTTTAATCAATTTT
1 TTAATTAAATTAAATTTAATCAATTTT
1209385 ACTCTCGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATTAAATTAAATTTAATCAATTTTT
Found at i:1209813 original size:26 final size:25
Alignment explanation
Indices: 1209769--1209848 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 25
1209759 ATTTAAATTT
*
1209769 TATTATTAATATAAAATAATTTTTAA
1 TATTATTTA-ATAAAATAATTTTTAA
1209795 TATTATTTAATAAATATAATAAATTTTTAA
1 TATTATTTAAT--A-A-AAT-AATTTTTAA
1209825 -ATTTATTTGAATAAAATAATTTTT
1 TA-TTATTT-AATAAAATAATTTTT
1209849 TTTAAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
25 2 0.04
26 15 0.33
27 4 0.09
28 2 0.04
29 5 0.11
30 15 0.33
31 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
TATTATTTAATAAAATAATTTTTAA
Found at i:1209820 original size:30 final size:32
Alignment explanation
Indices: 1209776--1209844 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 32
1209766 TTTTATTATT
*
1209776 AATATAAAATAATTTTT-AATATTATTT-AATA
1 AATATAATATAATTTTTAAAT-TTATTTGAATA
1209807 AATATAATA-AATTTTTAAATTTATTTGAATA
1 AATATAATATAATTTTTAAATTTATTTGAATA
1209838 AA-ATAAT
1 AATATAAT
1209845 TTTTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
AATATAATATAATTTTTAAATTTATTTGAATA
Found at i:1209858 original size:31 final size:30
Alignment explanation
Indices: 1209736--1209896 Score: 90
Period size: 30 Copynumber: 5.3 Consensus size: 30
1209726 TTGAAGCGAT
1209736 TTTATTTATATAAATTAAAT-TTTATT--TAAA
1 TTTATTTA-ATAAA-TAAATATTT-TTAATAAA
*
1209766 TTT-TATTATTAATATAAAATAATTTTTAAT--A
1 TTTAT-TTAATAA-AT-AAAT-ATTTTTAATAAA
*
1209797 -TTATTTAATAAATATAATAAATTTT--TAAA
1 TTTATTTAATAAATA-AAT-ATTTTTAATAAA
* *
1209826 TTTATTTGAATAAAATAATTTTTTTTAA-AAA
1 TTTATTT-AAT-AAATAAATATTTTTAATAAA
*
1209857 TTATATTTAATAGATAAATATTTTTAATAAA
1 TT-TATTTAATAAATAAATATTTTTAATAAA
1209888 TTTTATTTA
1 -TTTATTTA
1209897 TATTATATTT
Statistics
Matches: 103, Mismatches: 9, Indels: 37
0.69 0.06 0.25
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 17 0.17
30 42 0.41
31 26 0.25
32 15 0.15
33 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTATTTAATAAATAAATATTTTTAATAAA
Found at i:1210015 original size:17 final size:17
Alignment explanation
Indices: 1209987--1210027 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1209977 AATGTTATTG
1209987 TAATTA-ATTTTT-AAT
1 TAATTATATTTTTAAAT
1210002 TATATTATATTTTTAAAT
1 TA-ATTATATTTTTAAAT
1210020 TAATTATA
1 TAATTATA
1210028 ATAATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 4 0.17
17 12 0.52
18 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTATATTTTTAAAT
Found at i:1210044 original size:22 final size:22
Alignment explanation
Indices: 1209997--1210038 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1209987 TAATTAATTT
* *
1209997 TTAATTATATTATATTTTTAAA
1 TTAATTATAATATATTATTAAA
1210019 TTAATTATAATA-ATTATTAA
1 TTAATTATAATATATTATTAA
1210039 TCTTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATTATAATATATTATTAAA
Found at i:1213745 original size:15 final size:15
Alignment explanation
Indices: 1213727--1213775 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1213717 TATTATAATT
1213727 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
* *
1213742 TT-AAAATATTAAAT
1 TTAAAAATATAAAAA
*
1213756 TTAATAATATAAAAA
1 TTAAAAATATAAAAA
*
1213771 CTAAA
1 TTAAA
1213776 TTACTTCCTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:1213747 original size:14 final size:14
Alignment explanation
Indices: 1213730--1213775 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1213720 TATAATTTTA
1213730 AAAATATAAAAATT
1 AAAATATAAAAATT
* *
1213744 AAAATATTAAATTT
1 AAAATATAAAAATT
*
1213758 AATAATATAAAAACT
1 AA-AATATAAAAATT
1213773 AAA
1 AAA
1213776 TTACTTCCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:1213764 original size:29 final size:31
Alignment explanation
Indices: 1213717--1213775 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1213707 TTTTTTTATT
*
1213717 TATTATAATTTTAAAAATATAAAAATTAAAA
1 TATTATAATTTTAAAAATATAAAAACTAAAA
*
1213748 TATTA-AA-TTTAATAATATAAAAACTAAA
1 TATTATAATTTTAAAAATATAAAAACTAAA
1213776 TTACTTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 19 0.73
30 2 0.08
31 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
TATTATAATTTTAAAAATATAAAAACTAAAA
Found at i:1223180 original size:32 final size:32
Alignment explanation
Indices: 1223151--1223218 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 32
1223141 AATATAATTT
1223151 ACTATAAATATATTTTAAAATTTATATAATATAA
1 ACTATAAATATA--TTAAAATTTATATAATATAA
* *
1223185 ATTATTAATATATTAAAATTTATATAAATATAA
1 ACTATAAATATATTAAAATTTATAT-AATATAA
1223218 A
1 A
1223219 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 13 0.42
33 8 0.26
34 10 0.32
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
ACTATAAATATATTAAAATTTATATAATATAA
Found at i:1223186 original size:27 final size:27
Alignment explanation
Indices: 1223153--1223243 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
1223143 TATAATTTAC
1223153 TATAAATATATTTTAAAATTTATATAA
1 TATAAATATATTTTAAAATTTATATAA
1223180 TATAAATTATTAATATATTAAAATTTATATAAA
1 TATAAA-TA-T-AT-T-TTAAAATTTATAT-AA
*
1223213 TATAAA-ATATTTT-TAATATTATTATAA
1 TATAAATATATTTTAAAAT-TTA-TATAA
1223240 TATA
1 TATA
1223244 TTAAAATATA
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
26 3 0.05
27 17 0.31
28 6 0.11
29 3 0.05
30 3 0.05
31 2 0.04
32 13 0.24
33 8 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TATAAATATATTTTAAAATTTATATAA
Found at i:1223218 original size:17 final size:17
Alignment explanation
Indices: 1223166--1223220 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1223156 AAATATATTT
1223166 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
1223182 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
1223197 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
1223215 TAAAAT
1 TAAAAT
1223221 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1223675 original size:7 final size:7
Alignment explanation
Indices: 1223665--1223689 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1223655 AAATAAAAAA
1223665 TAAATTT
1 TAAATTT
1223672 TAAATTT
1 TAAATTT
1223679 TAAATTT
1 TAAATTT
1223686 TAAA
1 TAAA
1223690 AGTGTTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:1224451 original size:13 final size:13
Alignment explanation
Indices: 1224424--1224471 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1224414 TTTTTTTAAT
*
1224424 TAAAT-TTAAAGA
1 TAAATATTAAATA
1224436 TAAATATTAAATA
1 TAAATATTAAATA
*
1224449 TAAATATATTAATA
1 TAAATAT-TAAATA
1224463 TAATATATT
1 TAA-ATATT
1224472 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 5 0.16
13 13 0.42
14 9 0.29
15 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:1224488 original size:15 final size:15
Alignment explanation
Indices: 1224470--1224499 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1224460 ATATAATATA
*
1224470 TTTATTTTTAAATTT
1 TTTATATTTAAATTT
1224485 TTTATATTTAAATTT
1 TTTATATTTAAATTT
1224500 ATATAAAAAT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATATTTAAATTT
Found at i:1225908 original size:11 final size:10
Alignment explanation
Indices: 1225891--1226010 Score: 59
Period size: 8 Copynumber: 12.9 Consensus size: 10
1225881 AATAAAAATT
1225891 TTTTATATTA
1 TTTTATATTA
1225901 TATTTATATT-
1 T-TTTATATTA
*
1225911 TTTTAAATTA
1 TTTTATATTA
1225921 TTTTA-ATTA
1 TTTTATATTA
* *
1225930 TATTTAAAATA
1 T-TTTATATTA
*
1225941 TTTTTTA-T-
1 TTTTATATTA
*
1225949 TTTTATA-AA
1 TTTTATATTA
1225958 TTTTA-A-TA
1 TTTTATATTA
1225966 TTTTATA-TA
1 TTTTATATTA
1225975 -TTTATAACTTA
1 TTTTAT-A-TTA
1225986 -TTTA-ATT-
1 TTTTATATTA
1225993 TTTT-TATTA
1 TTTTATATTA
*
1226002 TATTATATT
1 TTTTATATT
1226011 TTAAAATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
8 26 0.29
9 26 0.29
10 19 0.21
11 18 0.20
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATTA
Found at i:1225913 original size:20 final size:19
Alignment explanation
Indices: 1225888--1225959 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
1225878 TAAAATAAAA
*
1225888 ATTTTTTATATTATATTTAT
1 ATTTTTTAAATTAT-TTTAT
1225908 ATTTTTTAAATTATTTTA-
1 ATTTTTTAAATTATTTTAT
* *
1225926 ATTATATTTAAAATATTTTTT
1 ATT-T-TTTAAATTATTTTAT
1225947 ATTTTTATAAATT
1 ATTTTT-TAAATT
1225960 TTAATATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.07
19 7 0.16
20 31 0.70
21 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTAAATTATTTTAT
Found at i:1225928 original size:9 final size:9
Alignment explanation
Indices: 1225887--1226014 Score: 51
Period size: 9 Copynumber: 14.2 Consensus size: 9
1225877 ATAAAATAAA
1225887 AATT-TTTT
1 AATTATTTT
1225895 ATATTATATTT
1 A-ATTAT-TTT
1225906 ATATT-TTTT
1 A-ATTATTTT
1225915 AAATTATTTT
1 -AATTATTTT
1225925 AATTATATTT
1 AATTAT-TTT
*
1225935 AAAATATTTT
1 -AATTATTTT
1225945 --TTATTTT
1 AATTATTTT
* *
1225952 TATAAATTTT
1 AAT-TATTTT
1225962 AA-TATTTT
1 AATTATTTT
1225970 -ATATATTTAT
1 AAT-TATTT-T
1225980 AACTTA-TTT
1 AA-TTATTTT
1225989 AATT-TTTT
1 AATTATTTT
* *
1225997 TATTATATT
1 AATTATTTT
1226006 -A-TATTTT
1 AATTATTTT
1226013 AA
1 AA
1226015 AATTTTTTAA
Statistics
Matches: 94, Mismatches: 8, Indels: 36
0.68 0.06 0.26
Matches are distributed among these distances:
7 12 0.13
8 16 0.17
9 27 0.29
10 22 0.23
11 16 0.17
12 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTATTTT
Found at i:1225962 original size:27 final size:25
Alignment explanation
Indices: 1225931--1226023 Score: 66
Period size: 25 Copynumber: 3.6 Consensus size: 25
1225921 TTTTAATTAT
*
1225931 ATTTAAAATATTTTTTATTTTTATAA
1 ATTTTAAAT-TTTTTTATTTTTATAA
* *
1225957 ATTTT-AATATTTTATATATTTATAA
1 ATTTTAAAT-TTTTTTATTTTTATAA
* *
1225982 CTTATTTAATTTTTTTATTATATTAT--
1 ATT-TTAAATTTTTTTATT-T-TTATAA
*
1226008 ATTTTAAAATTTTTTA
1 ATTTTAAATTTTTTTA
1226024 AATCATATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
25 31 0.57
26 15 0.28
27 4 0.07
28 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTTAAATTTTTTTATTTTTATAA
Found at i:1225968 original size:8 final size:9
Alignment explanation
Indices: 1225891--1225977 Score: 61
Period size: 9 Copynumber: 9.3 Consensus size: 9
1225881 AATAAAAATT
1225891 TTTTATATTA
1 TTTTATA-TA
*
1225901 TATTTATATT
1 T-TTTATATA
*
1225911 TTTTAAATTA
1 TTTTATA-TA
1225921 TTTTAATTATA
1 TTTT-A-TATA
* *
1225932 TTTAAAATA
1 TTTTATATA
*
1225941 TTTTTTAT-
1 TTTTATATA
*
1225949 TTTTATAAA
1 TTTTATATA
1225958 TTTTA-ATA
1 TTTTATATA
1225966 TTTTATATA
1 TTTTATATA
1225975 TTT
1 TTT
1225978 ATAACTTATT
Statistics
Matches: 59, Mismatches: 12, Indels: 13
0.70 0.14 0.15
Matches are distributed among these distances:
8 13 0.22
9 24 0.41
10 9 0.15
11 12 0.20
12 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:1226024 original size:34 final size:36
Alignment explanation
Indices: 1225958--1226024 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
1225948 TTTTTATAAA
* *
1225958 TTTTAATATTTTATATATTTATAACTTATTTAATTT
1 TTTTAATATATTATATATTTATAAATTATTTAATTT
* *
1225994 TTTTATTATATTATAT-TTTA-AAATTTTTTAA
1 TTTTAATATATTATATATTTATAAATTATTTAA
1226025 ATCATATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 9 0.33
35 4 0.15
36 14 0.52
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (36 bp):
TTTTAATATATTATATATTTATAAATTATTTAATTT
Found at i:1226396 original size:29 final size:29
Alignment explanation
Indices: 1226345--1226413 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 29
1226335 AATTTGATTA
1226345 TTTAA-AAAT-TTAAATATTAAATAAATAAT
1 TTTAATAAATATTAAATATTAAAT-AA-AAT
1226374 TTTAATAAATATTAAATA-T-AATAAAAT
1 TTTAATAAATATTAAATATTAAATAAAAT
*
1226401 TTTGATAAA-ATTA
1 TTTAATAAATATTA
1226414 TATGTTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 4 0.11
27 11 0.30
28 2 0.05
29 8 0.22
30 5 0.14
31 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TTTAATAAATATTAAATATTAAATAAAAT
Found at i:1226970 original size:24 final size:24
Alignment explanation
Indices: 1226943--1226997 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1226933 AAATTTTATT
1226943 TTATTTTATAAAATTTTA-AAATAA
1 TTATTTTA-AAAATTTTATAAATAA
* *
1226967 TTA-TTTAATATTTTTATTAAATAA
1 TTATTTTAAAAATTTTA-TAAATAA
1226991 TTATTTT
1 TTATTTT
1226998 GAACTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.27
23 4 0.15
24 12 0.46
25 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTTTAAAAATTTTATAAATAA
Found at i:1226973 original size:28 final size:27
Alignment explanation
Indices: 1226912--1226973 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
1226902 ATTTATTGAA
*
1226912 TATTTATTTTATAAAATAATAAAATTT
1 TATTTATTTTATAAAATAATAAAATAT
**
1226939 TATTTTATTTTATAAAATTTTAAAATAAT
1 TA-TTTATTTTATAAAATAATAAAAT-AT
1226968 TATTTA
1 TATTTA
1226974 ATATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.07
28 25 0.83
29 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTATTTTATAAAATAATAAAATAT
Found at i:1227143 original size:19 final size:18
Alignment explanation
Indices: 1227101--1227143 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1227091 TTATAATTAT
1227101 TTTATTTATTTTTTATAA
1 TTTATTTATTTTTTATAA
** *
1227119 AATATTTGTTTTATTATAA
1 TTTATTTATTTT-TTATAA
1227138 TTTATT
1 TTTATT
1227144 CATTCCAATG
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTATTTTTTATAA
Found at i:1228011 original size:27 final size:26
Alignment explanation
Indices: 1227981--1228035 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1227971 TTTTAAAAAA
1227981 TATTAAAAATTATTT-TATAATAATATT
1 TATTAAAAA-TATTTATATAATAAT-TT
**
1228008 TATTATTAATATTTATATAATAATTT
1 TATTAAAAATATTTATATAATAATTT
1228034 TA
1 TA
1228036 ATTGATTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTAAAAATATTTATATAATAATTT
Found at i:1228035 original size:13 final size:14
Alignment explanation
Indices: 1227991--1228035 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
1227981 TATTAAAAAT
1227991 TATTT-TATAATAA
1 TATTTATATAATAA
*
1228004 TATTTAT-TATTAA
1 TATTTATATAATAA
1228017 TATTTATATAATAA
1 TATTTATATAATAA
1228031 T-TTTA
1 TATTTA
1228036 ATTGATTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTTATATAATAA
Found at i:1228574 original size:22 final size:21
Alignment explanation
Indices: 1228539--1228579 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1228529 ATTAAAAATA
*
1228539 TTTATTATTAAATATTAATTT
1 TTTATTATTAAATAATAATTT
1228560 TTTATTATTTAAATAATAAT
1 TTTATTA-TTAAATAATAAT
1228580 ATAAATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATTATTAAATAATAATTT
Found at i:1229023 original size:15 final size:14
Alignment explanation
Indices: 1229000--1229033 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1228990 TACATCAAAC
*
1229000 AAAAGAATTTTAAA
1 AAAAAAATTTTAAA
1229014 TAAAAAAATTTTAAA
1 -AAAAAAATTTTAAA
1229029 AAAAA
1 AAAAA
1229034 TTTTGTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAAAATTTTAAA
Found at i:1232337 original size:23 final size:24
Alignment explanation
Indices: 1232299--1232343 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1232289 TTTAAAATTT
1232299 TTTTAATTTAAAATAAA-TTTTAA
1 TTTTAATTTAAAATAAAGTTTTAA
**
1232322 TTTTAATTTATTATAAAGTTTT
1 TTTTAATTTAAAATAAAGTTTT
1232344 TATGTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTAATTTAAAATAAAGTTTTAA
Found at i:1232475 original size:24 final size:24
Alignment explanation
Indices: 1232448--1232494 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1232438 TACTTCATTT
1232448 ATTTAAAATA-AATTTATAATTTTA
1 ATTTAAAATATAATTT-TAATTTTA
**
1232472 ATTTATTATATAATTTTAATTTT
1 ATTTAAAATATAATTTTAATTTT
1232495 TATATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTAAAATATAATTTTAATTTTA
Found at i:1232483 original size:18 final size:17
Alignment explanation
Indices: 1232462--1232523 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 17
1232452 AAAATAAATT
1232462 TATAATTTTAATTTATTA
1 TATAATTTTAATTT-TTA
1232480 TATAATTTTAATTTTTA
1 TATAATTTTAATTTTTA
1232497 TATTAATATTTAAATATTTT-
1 TA-TAAT-TTT-AAT-TTTTA
1232517 TATAATT
1 TATAATT
1232524 AAATTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.12
18 19 0.47
19 7 0.17
20 5 0.12
21 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATAATTTTAATTTTTA
Found at i:1232515 original size:22 final size:22
Alignment explanation
Indices: 1232490--1232535 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1232480 TATAATTTTA
1232490 ATTTTTAT-ATTAATATTTAAAT
1 ATTTTTATAATTAA-ATTTAAAT
1232512 ATTTTTATAATTAAATTTAAAT
1 ATTTTTATAATTAAATTTAAAT
1232534 AT
1 AT
1232536 AATATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTATAATTAAATTTAAAT
Found at i:1233261 original size:11 final size:10
Alignment explanation
Indices: 1233236--1233294 Score: 61
Period size: 9 Copynumber: 6.0 Consensus size: 10
1233226 ATTTTAATAA
1233236 ATTTATATA-
1 ATTTATATAT
1233245 ATTTATATCAT
1 ATTTATAT-AT
1233256 ATTTATATAT
1 ATTTATATAT
*
1233266 ATTT-TATTT
1 ATTTATATAT
1233275 A-TTATATTAT
1 ATTTATA-TAT
*
1233285 ATTTAAATAT
1 ATTTATATAT
1233295 TTTTTTGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
8 2 0.05
9 15 0.36
10 13 0.31
11 12 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1233282 original size:14 final size:15
Alignment explanation
Indices: 1233248--1233294 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1233238 TTATATAATT
*
1233248 TATATCATATTTATA
1 TATATTATATTTATA
*
1233263 TATATTTTATTTAT-
1 TATATTATATTTATA
*
1233277 TATATTATATTTAAA
1 TATATTATATTTATA
1233292 TAT
1 TAT
1233295 TTTTTTGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTATATTTATA
Found at i:1233339 original size:17 final size:16
Alignment explanation
Indices: 1233308--1233341 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1233298 TTTGTTGTAT
*
1233308 AATTATATTATATTTA
1 AATTATATTAAATTTA
1233324 AATTATTATTAAATTTA
1 AATTA-TATTAAATTTA
1233341 A
1 A
1233342 TAATTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATATTAAATTTA
Found at i:1238089 original size:14 final size:14
Alignment explanation
Indices: 1238070--1238113 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1238060 AATATAATAT
1238070 AATAAAATAATTAA
1 AATAAAATAATTAA
*
1238084 AATAAAAT-ATAAA
1 AATAAAATAATTAA
1238097 ATATAAAATAATATAA
1 A-ATAAAATAAT-TAA
1238113 A
1 A
1238114 TATATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 15 0.60
15 2 0.08
16 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAAATAATTAA
Found at i:1238092 original size:19 final size:19
Alignment explanation
Indices: 1238065--1238122 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1238055 ATGAAAATAT
*
1238065 AATATAATAAAATAATTAA
1 AATAAAATAAAATAATTAA
*
1238084 AATAAAATATAA-AATATAA
1 AATAAAATAAAATAAT-TAA
*
1238103 AATAATAT-AAATATATTAA
1 AATAAAATAAAATA-ATTAA
1238122 A
1 A
1238123 TTTATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.16
19 25 0.78
20 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAAATAAAATAATTAA
Found at i:1238130 original size:29 final size:29
Alignment explanation
Indices: 1238097--1238166 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1238087 AAAATATAAA
*
1238097 ATATAAAAT-AA-TATAAATATATTAAATTT
1 ATATAAAATAAATTATAAACATA--AAATTT
*
1238126 ATATATAATAAATTATAAACATAAAATTT
1 ATATAAAATAAATTATAAACATAAAATTT
* *
1238155 TTATAAATTAAA
1 ATATAAAATAAA
1238167 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 23 0.68
30 2 0.06
31 9 0.26
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
ATATAAAATAAATTATAAACATAAAATTT
Found at i:1238160 original size:17 final size:17
Alignment explanation
Indices: 1238138--1238181 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1238128 ATATAATAAA
1238138 TTATAAACATAAAAT-TT
1 TTATAAA-ATAAAATATT
*
1238155 TTATAAATTAAAATATT
1 TTATAAAATAAAATATT
1238172 TTA-AAAATAA
1 TTATAAAATAA
1238182 TTATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATAAAATAAAATATT
Found at i:1238730 original size:17 final size:18
Alignment explanation
Indices: 1238708--1238755 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
1238698 AATATAATAT
*
1238708 AAAATAT-TATAGTTTAA
1 AAAATATATAAAGTTTAA
*
1238725 AAAATAATATAAATTTTAA
1 AAAAT-ATATAAAGTTTAA
1238744 AAAATATATAAA
1 AAAATATATAAA
1238756 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATATATAAAGTTTAA
Found at i:1238765 original size:20 final size:19
Alignment explanation
Indices: 1238720--1238756 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1238710 AATATTATAG
1238720 TTTAAAAAATAATATAAAT
1 TTTAAAAAATAATATAAAT
1238739 TTTAAAAAAT-ATATAAAT
1 TTTAAAAAATAATATAAAT
1238757 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTAAAAAATAATATAAAT
Found at i:1239293 original size:22 final size:22
Alignment explanation
Indices: 1239234--1239295 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
1239224 TTTGATTTAT
* *
1239234 TAAAATAAAAT-ATAATAATAA
1 TAAAATAAAATAATTATAAAAA
* *
1239255 TAAAAT-AATTATTTTATAAAAA
1 TAAAATAAAATA-ATTATAAAAA
1239277 TAAAATAAAATAATTATAA
1 TAAAATAAAATAATTATAA
1239296 TATCAATTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.09
21 6 0.19
22 19 0.59
23 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAATAAAATAATTATAAAAA
Found at i:1240089 original size:7 final size:6
Alignment explanation
Indices: 1240054--1240085 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1240044 TTTTACATAA
1240054 TAAATT TAAA-T TAAA-T TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
1240086 ATTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:1240450 original size:17 final size:17
Alignment explanation
Indices: 1240403--1240451 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1240393 GTATTTTATT
1240403 TTATAATTATATTTAAAA
1 TTATAA-TATATTTAAAA
*
1240421 -TATTATATATTTATAAA
1 TTATAATATATTTA-AAA
1240438 TTATAATAT-TTTAA
1 TTATAATATATTTAA
1240452 TTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.33
17 11 0.41
18 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATATATTTAAAA
Found at i:1240463 original size:23 final size:24
Alignment explanation
Indices: 1240428--1240518 Score: 66
Period size: 23 Copynumber: 3.8 Consensus size: 24
1240418 AAATATTATA
1240428 TATTTATAAATTATAATATTTTAA-T
1 TATTTAT--ATTATAATATTTTAACT
*
1240453 TATTTATATTA-AATAAATTTTAACA
1 TATTTATATTATAAT--ATTTTAACT
* * *
1240478 TATTAATATTAT-TTATTTTATATT
1 TATTTATATTATAATATTTTA-ACT
1240502 TATTT-TATT-TAATATTT
1 TATTTATATTATAATATTT
1240519 AATATTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.08
23 19 0.36
24 12 0.23
25 18 0.34
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTATATTATAATATTTTAACT
Found at i:1240469 original size:32 final size:32
Alignment explanation
Indices: 1240411--1240471 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1240401 TTTTATAATT
*
1240411 ATATTTAAAATATTATATATTTATAAATTATA
1 ATATTTAAAATATTATATATTAATAAATTATA
* *
1240443 ATATTTTAATTATT-TATATTAAATAAATT
1 ATATTTAAAATATTATATATT-AATAAATT
1240472 TTAACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATTTAAAATATTATATATTAATAAATTATA
Found at i:1240481 original size:25 final size:25
Alignment explanation
Indices: 1240440--1240488 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1240430 TTTATAAATT
* *
1240440 ATAATATTTTAATTATTTATATTAA
1 ATAATATTTTAAATATTAATATTAA
1240465 ATAA-ATTTTAACATATTAATATTA
1 ATAATATTTTAA-ATATTAATATTA
1240489 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
ATAATATTTTAAATATTAATATTAA
Found at i:1240510 original size:16 final size:16
Alignment explanation
Indices: 1240480--1240519 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1240470 TTTTAACATA
1240480 TTAATA-TTA-TTTAT
1 TTAATATTTATTTTAT
*
1240494 TTTATATTTATTTTAT
1 TTAATATTTATTTTAT
1240510 TTAATATTTA
1 TTAATATTTA
1240520 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 5 0.23
15 3 0.14
16 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAATATTTATTTTAT
Found at i:1240833 original size:24 final size:25
Alignment explanation
Indices: 1240772--1240836 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
1240762 ATATAATCTA
* *
1240772 AAAAATAAACTATATAAATTAAAAT
1 AAAATTAAATTATATAAATTAAAAT
**
1240797 AAAATTATTTTAT-TAAA-TAAAATT
1 AAAATTAAATTATATAAATTAAAA-T
1240821 AAAATTAAATTATATA
1 AAAATTAAATTATATA
1240837 TATTTAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
23 5 0.16
24 16 0.50
25 11 0.34
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAATTAAATTATATAAATTAAAAT
Found at i:1240913 original size:2 final size:2
Alignment explanation
Indices: 1240906--1240937 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1240896 CTTTTGGTAC
1240906 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1240938 GGGACAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1241102 original size:15 final size:14
Alignment explanation
Indices: 1241077--1241131 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
1241067 CTCATAAAAA
1241077 AATAT-TAAAATAT
1 AATATATAAAATAT
1241090 AATATTATAAAATA-
1 AATA-TATAAAATAT
*
1241104 ATATAATATAAATTATT
1 A-AT-ATATAAAATA-T
1241121 AATATATAAAA
1 AATATATAAAA
1241132 ATTATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 24 0.71
16 3 0.09
17 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATAAAATAT
Found at i:1241135 original size:17 final size:18
Alignment explanation
Indices: 1241102--1241136 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1241092 TATTATAAAA
*
1241102 TAATATAATATAAATTAT
1 TAATATAATAAAAATTAT
1241120 TAATAT-ATAAAAATTAT
1 TAATATAATAAAAATTAT
1241137 ATAAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAATAAAAATTAT
Found at i:1241550 original size:15 final size:16
Alignment explanation
Indices: 1241525--1241558 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1241515 TTAGATAAAA
*
1241525 ATTTATAATTCGAGTT
1 ATTTATAATTCGAATT
1241541 ATTT-TAATTCGAATT
1 ATTTATAATTCGAATT
1241556 ATT
1 ATT
1241559 ATTTAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (16 bp):
ATTTATAATTCGAATT
Found at i:1242370 original size:17 final size:16
Alignment explanation
Indices: 1242348--1242398 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 16
1242338 TTTTAAGTTC
1242348 AATTAAAATTATTCTTT
1 AATTAAAATTATT-TTT
1242365 AATTAAAAAATTATTTTT
1 AATT--AAAATTATTTTT
1242383 AATTTAAAA-TATTTTT
1 AA-TTAAAATTATTTTT
1242399 TAATGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.23
17 8 0.26
18 5 0.16
19 11 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAAAATTATTTTT
Found at i:1242383 original size:18 final size:20
Alignment explanation
Indices: 1242352--1242391 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1242342 AAGTTCAATT
1242352 AAAATTATTCTTTAA-TTAA
1 AAAATTATTCTTTAATTTAA
1242371 AAAATTATT-TTTAATTTAA
1 AAAATTATTCTTTAATTTAA
1242390 AA
1 AA
1242392 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTATTCTTTAATTTAA
Found at i:1242411 original size:18 final size:17
Alignment explanation
Indices: 1242350--1242402 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
1242340 TTAAGTTCAA
*
1242350 TTAAAATTATTCTTTAA-
1 TTAAAA-TATTTTTTAAT
*
1242367 TTAAAAAATTATTTTTAAT
1 TTAAAATA-T-TTTTTAAT
1242386 TTAAAATATTTTTTAAT
1 TTAAAATATTTTTTAAT
1242403 GTTTAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 15 0.50
18 7 0.23
19 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAATATTTTTTAAT
Found at i:1242564 original size:22 final size:23
Alignment explanation
Indices: 1242539--1242603 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
1242529 TGATACAATT
1242539 ATATGATTAAAAAATA-AATAAA
1 ATATGATTAAAAAATATAATAAA
* *
1242561 ATATG-TTACAAAATATAATATA
1 ATATGATTAAAAAATATAATAAA
*
1242583 ATATAATATAAAAAATTATAA
1 ATATGAT-TAAAAAA-TATAA
1242604 AAATATAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.26
22 14 0.40
23 1 0.03
24 6 0.17
25 5 0.14
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (23 bp):
ATATGATTAAAAAATATAATAAA
Found at i:1242674 original size:31 final size:33
Alignment explanation
Indices: 1242606--1242675 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1242596 AATTATAAAA
* *
1242606 ATATAAGATGGATATATGAATATATCAAAATCT
1 ATATAAGATGAATATATAAATATATCAAAATCT
*
1242639 ATATAAGATGAAT-TATAAATTTAT-AAAAT-T
1 ATATAAGATGAATATATAAATATATCAAAATCT
1242669 CATATAA
1 -ATATAA
1242676 ATATATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.03
31 11 0.33
32 9 0.27
33 12 0.36
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (33 bp):
ATATAAGATGAATATATAAATATATCAAAATCT
Found at i:1243179 original size:2 final size:2
Alignment explanation
Indices: 1243165--1243211 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1243155 TTCATATGAT
*
1243165 TA TA TA TG T- TA TA TA -A 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
1243205 TA TA TA T
1 TA TA TA T
1243212 TACAATCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1244312 original size:9 final size:9
Alignment explanation
Indices: 1244291--1244344 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
1244281 AGTATATTTG
*
1244291 AATTAATTT
1 AATTAATTA
*
1244300 AATTGATTA
1 AATTAATTA
1244309 AATTAATTA
1 AATTAATTA
*
1244318 ATTTTAATT-
1 A-ATTAATTA
1244327 AATTAAATTA
1 AATT-AATTA
1244337 AATTAATT
1 AATTAATT
1244345 TTGTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 2 0.05
9 25 0.68
10 10 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
AATTAATTA
Found at i:1244326 original size:14 final size:14
Alignment explanation
Indices: 1244286--1244344 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1244276 GCATGAGTAT
*
1244286 ATTTGAATTAATTTA
1 ATTTTAATTAA-TTA
1244301 ATTGATTAAATTAATTA
1 ATT--TT-AATTAATTA
1244318 ATTTTAATTAATTA
1 ATTTTAATTAATTA
* *
1244332 AATTAAATTAATT
1 ATTTTAATTAATT
1244345 TTGTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 20 0.53
15 5 0.13
17 7 0.18
18 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
ATTTTAATTAATTA
Found at i:1244680 original size:17 final size:17
Alignment explanation
Indices: 1244652--1244693 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1244642 TTATTTATAA
1244652 AAAATAATTTAATAAATT
1 AAAAT-ATTTAATAAATT
1244670 AAAATATTTAATAAATT
1 AAAATATTTAATAAATT
*
1244687 TAAATAT
1 AAAATAT
1244694 AAAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATTTAATAAATT
Found at i:1244699 original size:17 final size:17
Alignment explanation
Indices: 1244662--1244745 Score: 51
Period size: 17 Copynumber: 4.6 Consensus size: 17
1244652 AAAATAATTT
**
1244662 AATAAATTAAAATATTT
1 AATAAATTAAAATATAA
*
1244679 AATAAATTTAAATATAA
1 AATAAATTAAAATATAA
** *
1244696 AATATTTTTAAAATTTAA
1 AATA-AATTAAAATATAA
* *
1244714 TAATAAATAAATTTAATTTAA
1 -AATAAATTAA---AATATAA
1244735 AATAAATTAAA
1 AATAAATTAAA
1244746 TTTATTAATT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
17 19 0.37
18 12 0.24
19 4 0.08
20 9 0.18
21 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAATTAAAATATAA
Found at i:1244719 original size:24 final size:24
Alignment explanation
Indices: 1244657--1244730 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
1244647 TATAAAAAAT
1244657 AATTTAATAAATTAAAATATTTAATA
1 AATTTAAT-AA-TAAAATATTTAATA
*
1244683 AATTTAA-ATATAAAATATTT-TTAA
1 AATTTAATA-ATAAAATATTTAAT-A
*
1244707 AATTTAATAATAAATAAATTTAAT
1 AATTTAATAATAAA-ATATTTAAT
1244731 TTAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 1 0.03
24 24 0.60
25 7 0.17
26 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AATTTAATAATAAAATATTTAATA
Found at i:1244731 original size:21 final size:21
Alignment explanation
Indices: 1244707--1244749 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1244697 ATATTTTTAA
1244707 AATTTAATAATAAA-TAAATTT
1 AATTTAA-AATAAATTAAATTT
1244728 AATTTAAAATAAATTAAATTT
1 AATTTAAAATAAATTAAATTT
1244749 A
1 A
1244750 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTAAAATAAATTAAATTT
Found at i:1244737 original size:16 final size:16
Alignment explanation
Indices: 1244718--1244749 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1244708 ATTTAATAAT
*
1244718 AAATAAATTTAATTTA
1 AAATAAATTAAATTTA
1244734 AAATAAATTAAATTTA
1 AAATAAATTAAATTTA
1244750 TTAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAAATTAAATTTA
Found at i:1246017 original size:30 final size:30
Alignment explanation
Indices: 1245964--1246043 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
1245954 AAATTTAAAA
1245964 TTAATTTT--TAAA-TAAATTA-TAAATTT
1 TTAATTTTAATAAATTAAATTATTAAATTT
*
1245990 TTAATTTTAATAAATTATATTATTAAATTT
1 TTAATTTTAATAAATTAAATTATTAAATTT
1246020 TT-ATTATTAATAAATTAAATTATT
1 TTAATT-TTAATAAATTAAATTATT
1246044 TATGTTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.17
28 4 0.09
29 9 0.19
30 26 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTAATTTTAATAAATTAAATTATTAAATTT
Found at i:1246021 original size:24 final size:24
Alignment explanation
Indices: 1245966--1246022 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
1245956 ATTTAAAATT
*
1245966 AATTTTTAAATAAATTATAAATTTTT
1 AATTTTT-AATAAATTAT-AATTTTA
1245992 AA-TTTTAATAAATTAT-ATTATTA
1 AATTTTTAATAAATTATAATT-TTA
1246015 AATTTTTA
1 AATTTTTA
1246023 TTATTAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 3 0.11
23 4 0.14
24 15 0.54
25 4 0.14
26 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTTTTAATAAATTATAATTTTA
Found at i:1246033 original size:17 final size:17
Alignment explanation
Indices: 1245982--1246035 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1245972 TAAATAAATT
1245982 ATAAATTTTTAATT-TTA
1 ATAAATTTTT-ATTATTA
1245999 ATAAA---TTA-TATTA
1 ATAAATTTTTATTATTA
*
1246012 TTAAATTTTTATTATTA
1 ATAAATTTTTATTATTA
1246029 ATAAATT
1 ATAAATT
1246036 AAATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 1 0.03
13 8 0.27
14 2 0.07
16 3 0.10
17 16 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAAATTTTTATTATTA
Found at i:1246564 original size:16 final size:17
Alignment explanation
Indices: 1246545--1246577 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1246535 TTAAAAAATT
1246545 AATATAATAA-AATTTA
1 AATATAATAATAATTTA
1246561 AATATAATAATAATTTA
1 AATATAATAATAATTTA
1246578 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAATAATAATTTA
Found at i:1248536 original size:21 final size:21
Alignment explanation
Indices: 1248512--1248555 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1248502 ATTGAGTTTG
*
1248512 AATTTGAAAAATATTAAACTT
1 AATTTGAAAAATAATAAACTT
* *
1248533 AATTTTAAAAATAATAAATTT
1 AATTTGAAAAATAATAAACTT
1248554 AA
1 AA
1248556 ACAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTGAAAAATAATAAACTT
Found at i:1251092 original size:30 final size:33
Alignment explanation
Indices: 1251028--1251092 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
1251018 AATTTTAAGA
1251028 TATTTATATTATTTTCATATTATTTTTCATATCG
1 TATTTATATTATTTT-ATATTATTTTTCATATCG
1251062 TATTTA-ATTATTTT-TATTATTTTT-ATATCG
1 TATTTATATTATTTTATATTATTTTTCATATCG
1251092 T
1 T
1251093 GTTTGTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 7 0.23
31 10 0.32
33 8 0.26
34 6 0.19
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (33 bp):
TATTTATATTATTTTATATTATTTTTCATATCG
Found at i:1252763 original size:2 final size:2
Alignment explanation
Indices: 1252756--1252798 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1252746 CTCATATACG
*
1252756 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA T- 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
1252796 TA T
1 TA T
1252799 CTAATATGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1253291 original size:20 final size:20
Alignment explanation
Indices: 1253268--1253305 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1253258 AATCCTTTGC
1253268 TCTTTTCATTAATTTATTCT
1 TCTTTTCATTAATTTATTCT
* *
1253288 TCTTTTTATTTATTTATT
1 TCTTTTCATTAATTTATT
1253306 TTTTATTTTT
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:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTCATTAATTTATTCT
Found at i:1253811 original size:14 final size:14
Alignment explanation
Indices: 1253792--1253847 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
1253782 ACAAATTAAA
* *
1253792 AAAATAATCATAAT
1 AAAATAATAAAAAT
1253806 AAAATAATAAAAAT
1 AAAATAATAAAAAT
*
1253820 ATAAATAAAAAAAAT
1 A-AAATAATAAAAAT
* *
1253835 -CAATAAAAAAAAT
1 AAAATAATAAAAAT
1253848 TATCTACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 12 0.32
14 13 0.35
15 12 0.32
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAATAAAAAT
Found at i:1253839 original size:13 final size:13
Alignment explanation
Indices: 1253807--1253847 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1253797 AATCATAATA
1253807 AAATAATAAAAATAT
1 AAATAA-AAAAA-AT
1253822 AAATAAAAAAAAT
1 AAATAAAAAAAAT
*
1253835 CAATAAAAAAAAT
1 AAATAAAAAAAAT
1253848 TATCTACTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 14 0.56
14 5 0.20
15 6 0.24
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:1254263 original size:5 final size:5
Alignment explanation
Indices: 1254253--1254277 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1254243 AACACCATCA
1254253 CCCAC CCCAC CCCAC CCCAC CCCAC
1 CCCAC CCCAC CCCAC CCCAC CCCAC
1254278 GGACTCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAC
Found at i:1259115 original size:16 final size:16
Alignment explanation
Indices: 1259094--1259128 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1259084 CGATTTCAAG
*
1259094 TTATTTTGAATTTAAA
1 TTATTTCGAATTTAAA
*
1259110 TTATTTCGATTTTAAA
1 TTATTTCGAATTTAAA
1259126 TTA
1 TTA
1259129 ATCAGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (16 bp):
TTATTTCGAATTTAAA
Found at i:1259322 original size:16 final size:16
Alignment explanation
Indices: 1259268--1259323 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
1259258 CAGGTTAATT
*
1259268 GTTC-AATTATTTTGG
1 GTTCAAATTATTTTGA
* *
1259283 GTTCAAATCATTTTAA
1 GTTCAAATTATTTTGA
* *
1259299 ATTTAAATTATTTTGA
1 GTTCAAATTATTTTGA
1259315 GTTCAAATT
1 GTTCAAATT
1259324 TGTTGATTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 4 0.13
16 27 0.87
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (16 bp):
GTTCAAATTATTTTGA
Found at i:1260236 original size:38 final size:34
Alignment explanation
Indices: 1260194--1260269 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 34
1260184 TATTTTCCAT
1260194 ATATTATAATATGTTTAA-AGTATTATATATTTATATAA
1 ATATTATAATATG-TTAATA--ATT-TATA-TTATATAA
1260232 ATA-T-TAATATGTTAATAATTTATATTATATAA
1 ATATTATAATATGTTAATAATTTATATTATATAA
1260264 ATATTA
1 ATATTA
1260270 AAAAATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
32 11 0.31
33 5 0.14
34 3 0.09
35 4 0.11
36 8 0.23
37 1 0.03
38 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (34 bp):
ATATTATAATATGTTAATAATTTATATTATATAA
Found at i:1260958 original size:16 final size:16
Alignment explanation
Indices: 1260939--1260972 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1260929 AAATTATCTG
*
1260939 AATCTAAAATGATTTA
1 AATCTAAAATGAATTA
1260955 AATCTAAAATGAATTA
1 AATCTAAAATGAATTA
1260971 AA
1 AA
1260973 ATCGAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
AATCTAAAATGAATTA
Found at i:1263925 original size:14 final size:13
Alignment explanation
Indices: 1263911--1263970 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 13
1263901 AATTGATTTG
1263911 AATTAATTTAATT
1 AATTAATTTAATT
* *
1263924 GATTAAATTAATT
1 AATTAATTTAATT
1263937 AA-T--TTTAATT
1 AATTAATTTAATT
1263947 AATTTAATTTAATT
1 AA-TTAATTTAATT
*
1263961 TATATAATTT
1 AAT-TAATTT
1263971 TTAAATTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
10 8 0.22
12 2 0.05
13 13 0.35
14 14 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:1264311 original size:28 final size:28
Alignment explanation
Indices: 1264279--1264333 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1264269 ATTTTTTCGA
1264279 TTAA-TTAAATAAGATTTAAAAATTTTAT
1 TTAATTTAAATAA-ATTTAAAAATTTTAT
* *
1264307 TTAATTTAATTAATTTTAAAAATTTTA
1 TTAATTTAAATAAATTTAAAAATTTTA
1264334 AAATCGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TTAATTTAAATAAATTTAAAAATTTTAT
Found at i:1264656 original size:20 final size:19
Alignment explanation
Indices: 1264627--1264666 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1264617 AATACATTAT
*
1264627 AATTTTAAATATAAATATAA
1 AATTTAAAATAT-AATATAA
1264647 AATTTAAAATATAATATAA
1 AATTTAAAATATAATATAA
1264666 A
1 A
1264667 TATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTAAAATATAATATAA
Found at i:1264668 original size:31 final size:30
Alignment explanation
Indices: 1264632--1264725 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 30
1264622 ATTATAATTT
*
1264632 TAAATATAAATATAAAATTTAAAATATAATA
1 TAAA-ATAAATATAAAATTTAAAATATTATA
*
1264663 T-AAAT--ATATAAATTTATCAAAAT-TTATA
1 TAAAATAAATATAAAATT-T-AAAATATTATA
1264691 TAAAATAAATTATCAAAATTTAAAA-ATTATA
1 TAAAATAAA-TAT-AAAATTTAAAATATTATA
1264722 TAAA
1 TAAA
1264726 TATTTAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
27 9 0.17
28 6 0.12
29 11 0.21
30 2 0.04
31 15 0.29
32 4 0.08
33 5 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAAATAAATATAAAATTTAAAATATTATA
Found at i:1264674 original size:20 final size:20
Alignment explanation
Indices: 1264633--1264674 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1264623 TTATAATTTT
*
1264633 AAATATAAATATAAAATTTA
1 AAATATAAATATAAAATATA
1264653 AAATAT-AATATAAATATATA
1 AAATATAAATATAAA-ATATA
1264673 AA
1 AA
1264675 TTTATCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAATATAAAATATA
Found at i:1264675 original size:19 final size:19
Alignment explanation
Indices: 1264632--1264675 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1264622 ATTATAATTT
*
1264632 TAAATATAAATATAAAATT
1 TAAATATAAATATAAAATA
1264651 TAAA-ATATAATATAAATATA
1 TAAATATA-AATATAAA-ATA
1264671 TAAAT
1 TAAAT
1264676 TTATCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATAAATATAAAATA
Found at i:1264692 original size:33 final size:30
Alignment explanation
Indices: 1264632--1264725 Score: 83
Period size: 33 Copynumber: 3.1 Consensus size: 30
1264622 ATTATAATTT
1264632 TAAATATAAA-TATAAAATTT--AAA--ATA
1 TAAA-ATAAATTATAAAATTTAAAAATTATA
*
1264658 TAATATAAA-TATATAAATTTATCAAAATTTATA
1 TAAAATAAATTATA-AAATTTA--AAAA-TTATA
1264691 TAAAATAAATTATCAAAATTTAAAAATTATA
1 TAAAATAAATTAT-AAAATTTAAAAATTATA
1264722 TAAA
1 TAAA
1264726 TATTTAATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
25 9 0.16
26 9 0.16
30 3 0.05
31 9 0.16
32 4 0.07
33 11 0.20
34 10 0.18
35 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAAATAAATTATAAAATTTAAAAATTATA
Found at i:1264692 original size:53 final size:52
Alignment explanation
Indices: 1264635--1264793 Score: 134
Period size: 53 Copynumber: 3.0 Consensus size: 52
1264625 ATAATTTTAA
1264635 ATATAAATATAAAATTTAAAATATAATATAAATATATAAATTTATCAAAATTT
1 ATATAAATATAAAATTTAAAAT-TAATATAAATATATAAATTTATCAAAATTT
* *
1264688 ATATAAA-AT-AAATTATCAAAATTTAA-A-AATTATATAAATATT-T-AATATTTT
1 ATATAAATATAAAATT-T-AAAA-TTAATATAAATATATAAAT-TTATCAA-AATTT
* * ** *
1264739 AAATATAATTATAACACATAAAATTAATATAAATATTTAAA-TTATCAAAATTT
1 --ATATAAATATAAAATTTAAAATTAATATAAATATATAAATTTATCAAAATTT
1264792 AT
1 AT
1264794 TTTTATTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 28
0.69 0.07 0.23
Matches are distributed among these distances:
50 2 0.02
51 23 0.27
52 12 0.14
53 30 0.36
54 15 0.18
55 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (52 bp):
ATATAAATATAAAATTTAAAATTAATATAAATATATAAATTTATCAAAATTT
Found at i:1265252 original size:19 final size:21
Alignment explanation
Indices: 1265202--1265253 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
1265192 ATTTTTATTT
1265202 AATTTTAATTATAAAATATATA
1 AATTTTAA-TATAAAATATATA
*
1265224 AATATTAATATAAAATA-A-A
1 AATTTTAATATAAAATATATA
*
1265243 ATTTTTAATAT
1 AATTTTAATAT
1265254 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
21 9 0.33
22 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTTAATATAAAATATATA
Found at i:1265648 original size:14 final size:13
Alignment explanation
Indices: 1265620--1265675 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1265610 GATAAATATT
1265620 ATTTTT-AAAAT-
1 ATTTTTAAAAATA
1265631 -TTTTTAAAAATA
1 ATTTTTAAAAATA
*
1265643 ACTTTTAAAAAATA
1 A-TTTTTAAAAATA
* *
1265657 ATTATTAATAATA
1 ATTTTTAAAAATA
1265670 ATTTTT
1 ATTTTT
1265676 TATTTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 5 0.14
11 5 0.14
13 14 0.39
14 12 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTTAAAAATA
Found at i:1266229 original size:2 final size:2
Alignment explanation
Indices: 1266188--1266221 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1266178 TATTATCAGT
*
1266188 TA TA TA TA CA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1266222 GGATATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1266633 original size:19 final size:19
Alignment explanation
Indices: 1266611--1266649 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1266601 TTTAAAGTTA
*
1266611 AAATAACTCTATATTTTTT
1 AAATAAATCTATATTTTTT
* *
1266630 AAATAAATTTTTATTTTTT
1 AAATAAATCTATATTTTTT
1266649 A
1 A
1266650 TTATATTTAA
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:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATAAATCTATATTTTTT
Found at i:1266672 original size:16 final size:16
Alignment explanation
Indices: 1266653--1266713 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
1266643 TTTTTTATTA
1266653 TATTTAAATAAATTTT
1 TATTTAAATAAATTTT
** *
1266669 TATTTTTTATAAGTTTT
1 TA-TTTAAATAAATTTT
* *
1266686 TACTT-AATTAATTTT
1 TATTTAAATAAATTTT
1266701 TATTTGAAATAAA
1 TATTT-AAATAAA
1266714 ATATTAATTC
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
15 11 0.33
16 4 0.12
17 18 0.55
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (16 bp):
TATTTAAATAAATTTT
Found at i:1266694 original size:28 final size:28
Alignment explanation
Indices: 1266627--1266680 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1266617 CTCTATATTT
*
1266627 TTTAAATAAATTTTTATTTTTTATTATA
1 TTTAAATAAATTTTTATTTTTTATAATA
1266655 TTTAAATAAATTTTTATTTTTTATAA
1 TTTAAATAAATTTTTATTTTTTATAA
1266681 GTTTTTACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTAAATAAATTTTTATTTTTTATAATA
Found at i:1266792 original size:30 final size:30
Alignment explanation
Indices: 1266726--1266817 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
1266716 ATTAATTCAT
* * * *
1266726 TTTAAGAATTTATTTGAATATAAATGATAA
1 TTTAAAAATTTATTTGAATATAATTTAAAA
*
1266756 -TTAAAAATTTATTTGAGTATAATTTAAAA
1 TTTAAAAATTTATTTGAATATAATTTAAAA
*
1266785 TTTAAAAATTTATTTAAATAT-ATATTAAAA
1 TTTAAAAATTTATTTGAATATAAT-TTAAAA
1266815 TTT
1 TTT
1266818 TAAATAGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.49
30 27 0.51
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTAAAAATTTATTTGAATATAATTTAAAA
Found at i:1266945 original size:19 final size:18
Alignment explanation
Indices: 1266901--1266956 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1266891 AAATTTTTAT
1266901 ATTTTTATTATATTTAAATAA
1 ATTTTTATT-T-TTT-AATAA
1266922 ATTTTTATCTTTTTAATAA
1 ATTTTTAT-TTTTTAATAA
*
1266941 GTTTTTATTTTTTAAT
1 ATTTTTATTTTTTAAT
1266957 TTTCCTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 8 0.24
19 12 0.36
20 3 0.09
21 9 0.27
22 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTTATTTTTTAATAA
Found at i:1267009 original size:274 final size:273
Alignment explanation
Indices: 1266659--1267442 Score: 1047
Period size: 295 Copynumber: 2.8 Consensus size: 273
1266649 ATTATATTTA
* * * *
1266659 AATAAATTTTTATTTTTTATAAGTTTTTACTTAATTAATTTTTATTTGAAATAAAATATTAATTC
1 AATAAGTTTTTA-TTTTT-TAA--TTTTCCTCAATTAATTTTTATTTGAAATAAAATATTAATTT
*
1266724 ATTTTAAGAATTTATTTGAATATAAATGATAA-TTAAAAATTTATTTGAGTATAATTTAAAATTT
62 ATTTTAAGAATTTATTTAAATATAAATGATAAGTTAAAAATTTATTTGAGTATAATTTAAAATTT
1266788 AAAAATTTATTTAAATATATATTAAAATTTTAAATAGTTTTTCATATTATTATTATTATTATTAT
127 AAAAATTTATTTAAATATATATTAAAATTTTAAATAGTTTTTCA-ATTATTATTATTATTATTAT
*
1266853 TTTAGCAATTTAAAGGGAATAACTCTATTTTTTAAAATAAATTTTTATATTTTTATTATATTTAA
191 TTTAGCAATTTAAAGGGAATAACTCTATTTTTTAAAATAAACTTTTATATTTTTATTATATTTAA
1266918 ATAAATTTTTATCTTTTT
256 ATAAATTTTTATCTTTTT
1266936 AATAAGTTTTTATTTTTTAATTTTCCTCAATTAATTTTTATTTGAAATAAAAATATTAATTTATT
1 AATAAGTTTTTATTTTTTAATTTTCCTCAATTAATTTTTATTTGAAAT-AAAATATTAATTTATT
*
1267001 TTAAGAATTTATTTAAATATAAATGATAAGTT-AAAATTTATTTGTGTATAATTTAAAATTTAAA
65 TTAAGAATTTATTTAAATATAAATGATAAGTTAAAAATTTATTTGAGTATAATTTAAAATTTAAA
* * *
1267065 AATTTATTTAAATATATATTAAAATTTATTTAAATGTAATAAAAAATAATAAATTTAAGAGTTTT
130 AATTTATTTAAATATATATTAAAA--T-TTT--A---AAT----AGT--T---TTTCA-A--TTA
*
1267130 TCATATTATTATTATTATTTTAGCAATTTAAAGGGAATAACTCTATTTTTTTAAATAAACTTTTA
175 T--TATTATTATTATTATTTTAGCAATTTAAAGGGAATAACTCTATTTTTTAAAATAAACTTTTA
1267195 TATTTTTATTATATTTAAATAAATTTTTATCTTTTT
238 TATTTTTATTATATTTAAATAAATTTTTATCTTTTT
* * *
1267231 AATAAGTTTTTGTTTTTTAATTTTCCTCAACTAATTTTTATTTTAAATAAAATATTAATTTATTT
1 AATAAGTTTTTATTTTTTAATTTTCCTCAATTAATTTTTATTTGAAATAAAATATTAATTTATTT
* *
1267296 TAAAAATTTATTTAAATATAAATGATAAGTTAAAAAATTATTTGAGTATAATTTAAAATTTAAAA
66 TAAGAATTTATTTAAATATAAATGATAAGTTAAAAATTTATTTGAGTATAATTTAAAATTTAAAA
* * * *
1267361 TTTTATTTAAATATAATAAAATTAATAAAATTT-AAGAGTTTTTC--TTATTATTATTATTATCA
131 ATTTATTTAAATAT-AT---ATT-A-AAATTTTAAATAGTTTTTCAATTATTATTATTATTATTA
1267423 TTTTAGCAATTTAAAGGGAA
190 TTTTAGCAATTTAAAGGGAA
1267443 AGCTTGGACA
Statistics
Matches: 452, Mismatches: 25, Indels: 61
0.84 0.05 0.11
Matches are distributed among these distances:
273 26 0.06
274 98 0.22
275 5 0.01
276 39 0.09
277 14 0.03
278 3 0.01
279 1 0.00
282 3 0.01
283 3 0.01
286 3 0.01
288 3 0.01
291 5 0.01
292 2 0.00
293 3 0.01
294 47 0.10
295 185 0.41
296 2 0.00
298 3 0.01
299 3 0.01
300 1 0.00
301 3 0.01
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (273 bp):
AATAAGTTTTTATTTTTTAATTTTCCTCAATTAATTTTTATTTGAAATAAAATATTAATTTATTT
TAAGAATTTATTTAAATATAAATGATAAGTTAAAAATTTATTTGAGTATAATTTAAAATTTAAAA
ATTTATTTAAATATATATTAAAATTTTAAATAGTTTTTCAATTATTATTATTATTATTATTTTAG
CAATTTAAAGGGAATAACTCTATTTTTTAAAATAAACTTTTATATTTTTATTATATTTAAATAAA
TTTTTATCTTTTT
Found at i:1267038 original size:29 final size:29
Alignment explanation
Indices: 1267001--1267080 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
1266991 TTAATTTATT
*
1267001 TTAAGAATTTATTTAAATATAAATGATAAG
1 TTAA-AATTTATTTAAATATAAATGAAAAG
*** * * *
1267031 TTAAAATTTATTTGTGTATAATTTAAAAT
1 TTAAAATTTATTTAAATATAAATGAAAAG
1267060 TTAAAAATTTATTTAAATATA
1 TT-AAAATTTATTTAAATATA
1267081 TATTAAAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.46
Consensus pattern (29 bp):
TTAAAATTTATTTAAATATAAATGAAAAG
Found at i:1267075 original size:12 final size:12
Alignment explanation
Indices: 1267058--1267098 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1267048 ATAATTTAAA
1267058 ATTTAAAAATTT
1 ATTTAAAAATTT
* *
1267070 ATTTAAATATAT
1 ATTTAAAAATTT
1267082 A-TT-AAAATTT
1 ATTTAAAAATTT
1267092 ATTTAAA
1 ATTTAAA
1267099 TGTAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 6 0.26
11 4 0.17
12 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTAAAAATTT
Found at i:1267087 original size:30 final size:29
Alignment explanation
Indices: 1267000--1267092 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 29
1266990 ATTAATTTAT
* * *
1267000 TTTAAGAATTTATTTAAATATAAATGATAA
1 TTTAAAAATTTATTTAAATAT-AATTAAAA
* ***
1267030 GTT-AAAATTTATTTGTGTATAATTTAAAA
1 TTTAAAAATTTATTTAAATATAA-TTAAAA
1267059 TTTAAAAATTTATTTAAATATATATTAAAA
1 TTTAAAAATTTATTTAAATATA-ATTAAAA
1267089 TTTA
1 TTTA
1267093 TTTAAATGTA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 2 0.04
29 19 0.39
30 27 0.55
31 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (29 bp):
TTTAAAAATTTATTTAAATATAATTAAAA
Found at i:1267111 original size:22 final size:22
Alignment explanation
Indices: 1267061--1267109 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1267051 ATTTAAAATT
1267061 TAAAAATTTATTTAAATATATA
1 TAAAAATTTATTTAAATATATA
* *
1267083 TTAAAATTTATTTAAATGTA-A
1 TAAAAATTTATTTAAATATATA
1267104 TAAAAA
1 TAAAAA
1267110 ATAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAATTTATTTAAATATATA
Found at i:1267240 original size:19 final size:18
Alignment explanation
Indices: 1267196--1267251 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1267186 AAACTTTTAT
1267196 ATTTTTATTATATTTAAATAA
1 ATTTTTATT-T-TTT-AATAA
1267217 ATTTTTATCTTTTTAATAA
1 ATTTTTAT-TTTTTAATAA
* *
1267236 GTTTTTGTTTTTTAAT
1 ATTTTTATTTTTTAAT
1267252 TTTCCTCAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.25
19 11 0.34
20 3 0.09
21 9 0.28
22 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
ATTTTTATTTTTTAATAA
Found at i:1267377 original size:30 final size:29
Alignment explanation
Indices: 1267294--1267394 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 29
1267284 ATTAATTTAT
* *
1267294 TTTAAAAATTTATTTAAATATAAATGATAA
1 TTTAAAAATTTATTTAAATAT-AATTAAAA
* * * *
1267324 GTTAAAAAATTATTTGAGTATAATTTAAAA
1 TTTAAAAATTTATTTAAATATAA-TTAAAA
*
1267354 TTTAAAATTTTATTTAAATATAA-TAAAA
1 TTTAAAAATTTATTTAAATATAATTAAAA
*
1267382 TTAATAAAATTTA
1 TTTA-AAAATTTA
1267395 AGAGTTTTTC
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
28 8 0.14
29 9 0.16
30 39 0.70
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTAAAAATTTATTTAAATATAATTAAAA
Done.