Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold37
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: 836391
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:147415 original size:21 final size:21
Alignment explanation
Indices: 147398--147439 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
147388 ATTATTTAGA
147398 GTTAAATTATTTTAATTTGAT
1 GTTAAATTATTTTAATTTGAT
*
147419 TTTAAATTATTTTAAATTTGA
1 GTTAAATTATTTT-AATTTGA
147440 ATAATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
GTTAAATTATTTTAATTTGAT
Found at i:147430 original size:10 final size:10
Alignment explanation
Indices: 147399--147436 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
147389 TTATTTAGAG
147399 TTAAATTATT
1 TTAAATTATT
*
147409 TTAATTTGATT
1 TTAAATT-ATT
147420 TTAAATTATT
1 TTAAATTATT
147430 TTAAATT
1 TTAAATT
147437 TGAATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
TTAAATTATT
Found at i:149268 original size:2 final size:2
Alignment explanation
Indices: 149261--149300 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
149251 AAATAAGACA
149261 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
149301 TACAAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149444 original size:19 final size:20
Alignment explanation
Indices: 149408--149454 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
149398 AAAATAATTA
149408 TTTTTTAAAATAATTTAATC
1 TTTTTTAAAATAATTTAATC
*
149428 TTTTTTAAAATAA-TTAATT
1 TTTTTTAAAATAATTTAATC
149447 TTTTTTAA
1 TTTTTTAA
149455 CATATCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTTAAAATAATTTAATC
Found at i:149873 original size:24 final size:24
Alignment explanation
Indices: 149829--149874 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
149819 TGGAAAATTC
**
149829 ATTTTTTAAAAAAATTTAAAAAGG
1 ATTTTTTAAAAAAATAAAAAAAGG
149853 ATTTTTTAAAAAAATAAAAAAA
1 ATTTTTTAAAAAAATAAAAAAA
149875 AAAACTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
ATTTTTTAAAAAAATAAAAAAAGG
Found at i:150573 original size:2 final size:2
Alignment explanation
Indices: 150566--150598 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
150556 TTAAAACCAA
150566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
150599 GATTTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:151668 original size:34 final size:33
Alignment explanation
Indices: 151620--151840 Score: 266
Period size: 34 Copynumber: 6.5 Consensus size: 33
151610 TGGTAAAAAC
*
151620 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
151653 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
151687 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
151721 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
151755 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
151789 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
151823 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
151841 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 133 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:151736 original size:68 final size:67
Alignment explanation
Indices: 151622--151840 Score: 296
Period size: 68 Copynumber: 3.2 Consensus size: 67
151612 GTAAAAACCA
* * *
151622 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
151687 CAC
65 CAC
* * * *
151690 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
151755 CTC
65 CAC
* * * *
151758 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
151823 CA-
65 CAC
151825 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
151841 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 17 0.13
68 114 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:151764 original size:102 final size:101
Alignment explanation
Indices: 151620--151840 Score: 352
Period size: 102 Copynumber: 2.2 Consensus size: 101
151610 TGGTAAAAAC
* *
151620 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
151685 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
151721 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
151786 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
151823 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
151841 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:156302 original size:34 final size:33
Alignment explanation
Indices: 156254--156474 Score: 232
Period size: 34 Copynumber: 6.5 Consensus size: 33
156244 TGGTAAAAAC
156254 CACCATTTAATCAACAAT-GTCAACCTACCAAAT
1 CACCATTTAATCAACAATGGT-AACCTACCAAAT
*
156287 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
156321 CACTCATTTAATCAATAATGGTAAACTACTAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
** * *
156355 TTCTCATTTAATCAACAATGGTAAGCTATCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
156389 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
156423 CACCCTATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CC-ATTTAATCAACAATGGTAACCTACCAAAT
156458 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
156475 AATTTAGAAT
Statistics
Matches: 157, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
33 17 0.11
34 108 0.69
35 32 0.20
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:156399 original size:102 final size:102
Alignment explanation
Indices: 156254--156474 Score: 320
Period size: 102 Copynumber: 2.2 Consensus size: 102
156244 TGGTAAAAAC
* *
156254 CACCATTTAATCAACAATGTCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGTCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
156319 ATCACTC-ATTTAATCAATAATGGTAAACTACTAAAT
66 ATCACCCTATTTAATCAACAATGGTAAACTACCAAAT
** * * *
156355 TTCTCATTTAATCAACAATGGT-AAGCTATCAAATCTCCCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAAT-GTCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACC
156419 AAATCACCCTATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCTATTTAATCAACAATGGTAAACTACCAAAT
156458 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
156475 AATTTAGAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
101 1 0.01
102 74 0.70
103 30 0.29
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (102 bp):
CACCATTTAATCAACAATGTCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCTATTTAATCAACAATGGTAAACTACCAAAT
Found at i:156581 original size:16 final size:16
Alignment explanation
Indices: 156560--156590 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
156550 TTAATAGTTT
156560 TTATTTAATTAATTAA
1 TTATTTAATTAATTAA
156576 TTATTTAATTAATTA
1 TTATTTAATTAATTA
156591 TAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTTAATTAATTAA
Found at i:157850 original size:18 final size:18
Alignment explanation
Indices: 157811--157853 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
157801 AAGTACTTAT
*
157811 AATATATAATATTTATTTA
1 AATAT-TAATATTTATTAA
157830 AATATTAATTATTT-TTAA
1 AATATTAA-TATTTATTAA
157848 AATATT
1 AATATT
157854 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTAATATTTATTAA
Found at i:161584 original size:15 final size:17
Alignment explanation
Indices: 161550--161594 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
161540 GTTTTAAATA
*
161550 TTATATATTATATAATT
1 TTATATATCATATAATT
161567 TTATATATCA-ATAA-T
1 TTATATATCATATAATT
161582 TTATA-AT-ATATAA
1 TTATATATCATATAA
161595 ATTAATACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 6 0.23
15 6 0.23
16 4 0.15
17 9 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATATCATATAATT
Found at i:164329 original size:2 final size:2
Alignment explanation
Indices: 164322--164347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
164312 TAAAGTTTAC
164322 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
164348 TTAAGCTAAT
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:164791 original size:6 final size:7
Alignment explanation
Indices: 164773--164798 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
164763 AAAAACTCTA
164773 TAAAAAT
1 TAAAAAT
164780 TAAAAAT
1 TAAAAAT
164787 TAAAAAT
1 TAAAAAT
164794 TAAAA
1 TAAAA
164799 CTTATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:165847 original size:4 final size:4
Alignment explanation
Indices: 165838--165875 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
165828 ATTTTTAAAA
165838 TAAT TAAT TAAT TAAT TAAT TAAAT TAAT TAAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT T-AAT TAAT T-AAT TAAT
165876 AATCAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:165849 original size:8 final size:9
Alignment explanation
Indices: 165832--165875 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
165822 ATTTAAATTT
*
165832 TTAAAATAA
1 TTAAATTAA
165841 TT-AATTAA
1 TTAAATTAA
165849 TT-AATTAA
1 TTAAATTAA
165857 TTAAATTAA
1 TTAAATTAA
165866 TTAAATTAA
1 TTAAATTAA
165875 T
1 T
165876 AATCAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
8 15 0.45
9 18 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAAATTAA
Found at i:166532 original size:35 final size:33
Alignment explanation
Indices: 166462--166583 Score: 126
Period size: 35 Copynumber: 3.7 Consensus size: 33
166452 AAATAAATAT
*
166462 AATATAAAACAAT-TAAA-ATA-T-AAATATAA
1 AATATAAAATAATATAAATATATTAAAATATAA
*
166491 AATATAAGATAATATAAATATATTAAAATTTATAA
1 AATATAAAATAATATAAATATATTAAAA--TATAA
* * *
166526 AATATAAAATATTTTAAATATAATTATAATATAA
1 AATATAAAATAATATAAATAT-ATTAAAATATAA
*
166560 ATATATAATATAATATAAATATAT
1 A-ATATAAAATAATATAAATATAT
166584 AAATCAATCA
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
29 11 0.14
30 4 0.05
31 3 0.04
32 1 0.01
33 3 0.04
34 8 0.11
35 40 0.53
36 6 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
AATATAAAATAATATAAATATATTAAAATATAA
Found at i:168736 original size:2 final size:2
Alignment explanation
Indices: 168729--168759 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
168719 ATTAAGAGCA
168729 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 A
168760 GAACCCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:175653 original size:2 final size:2
Alignment explanation
Indices: 175646--175678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
175636 TACCACTCTC
175646 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
175679 AGAAATCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:179477 original size:32 final size:32
Alignment explanation
Indices: 179436--179501 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
179426 ATTCTGGAGC
179436 AGTAAGGCACATGCACAGATGAAGTTAAGAGA
1 AGTAAGGCACATGCACAGATGAAGTTAAGAGA
* *
179468 AGTAAGGCACATGTATAGATGAAGTTAAGAGA
1 AGTAAGGCACATGCACAGATGAAGTTAAGAGA
179500 AG
1 AG
179502 CACTGAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.29, T:0.18
Consensus pattern (32 bp):
AGTAAGGCACATGCACAGATGAAGTTAAGAGA
Found at i:189277 original size:28 final size:25
Alignment explanation
Indices: 189214--189278 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
189204 AATACTATAA
189214 TTTTTTTAGT-AAAAAAAATGGTAG
1 TTTTTTTAGTGAAAAAAAATGGTAG
*
189238 TTTTTCTT--TGAAGTAAAAAGTGGATAG
1 TTTTT-TTAGTGAA--AAAAAATGG-TAG
189265 TTTTTTTAGTGAAA
1 TTTTTTTAGTGAAA
189279 TAATGGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
23 1 0.03
24 7 0.21
25 2 0.06
26 11 0.33
27 8 0.24
28 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (25 bp):
TTTTTTTAGTGAAAAAAAATGGTAG
Found at i:189720 original size:21 final size:21
Alignment explanation
Indices: 189672--189716 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
189662 GAGATATAAA
189672 TATTTT-TAAAATATTATTTT
1 TATTTTATAAAATATTATTTT
*
189692 TAATTTATAAAATA-T-TTTT
1 TATTTTATAAAATATTATTTT
189711 TATTTT
1 TATTTT
189717 TTATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATAAAATATTATTTT
Found at i:192646 original size:33 final size:33
Alignment explanation
Indices: 192580--192646 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
192570 AGTTTAGTGG
* * *
192580 AAATCTTTGTTTCTGAATGTCATGCTCTTAGGT
1 AAATCTTTGTTACTGAATGTCATACTCTGAGGT
* **
192613 AAATCTTTGTTACTGAATTTTGTACTCTGAGGT
1 AAATCTTTGTTACTGAATGTCATACTCTGAGGT
192646 A
1 A
192647 TTGTGACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (33 bp):
AAATCTTTGTTACTGAATGTCATACTCTGAGGT
Found at i:196955 original size:11 final size:11
Alignment explanation
Indices: 196939--196991 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
196929 AATATACTCA
196939 TATTTAATATT
1 TATTTAATATT
196950 TATTTAA-ATT
1 TATTTAATATT
196960 TAATTTAAAATATT
1 T-ATTT--AATATT
* *
196974 TAATTAATAAT
1 TATTTAATATT
196985 TATTTAA
1 TATTTAA
196992 ATAATCATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 4 0.11
11 22 0.63
13 5 0.14
14 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTTAATATT
Found at i:196989 original size:24 final size:24
Alignment explanation
Indices: 196944--196992 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
196934 ACTCATATTT
* *
196944 AATATTTATTTAAATTTAATTTAA
1 AATATTTAATTAAAATTAATTTAA
196968 AATATTTAATTAATAATT-ATTTAA
1 AATATTTAATTAA-AATTAATTTAA
196992 A
1 A
196993 TAATCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATTTAATTAAAATTAATTTAA
Found at i:196990 original size:15 final size:14
Alignment explanation
Indices: 196957--197005 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
196947 ATTTATTTAA
196957 ATTTAATTTAA-AAT
1 ATTTAA-TTAATAAT
196971 ATTTAATTAATAATT
1 ATTTAATTAATAA-T
* *
196986 ATTTAAATAATCAT
1 ATTTAATTAATAAT
197000 ATTTAA
1 ATTTAA
197006 GGGACGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAATTAATAAT
Found at i:197553 original size:28 final size:25
Alignment explanation
Indices: 197520--197581 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 25
197510 AATATAAAAT
*
197520 ATAAAATAATATTTAAAATATTATGCA
1 ATAAAATAATATATAAAATA-TATG-A
197547 CATAAAATAAATATATAAAATATATGA
1 -ATAAAAT-AATATATAAAATATATGA
197574 ATAAAATA
1 ATAAAATA
197582 TAAATCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 1 0.03
26 7 0.22
27 1 0.03
28 11 0.34
29 12 0.38
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAAAATAATATATAAAATATATGA
Found at i:197582 original size:13 final size:14
Alignment explanation
Indices: 197533--197583 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
197523 AAATAATATT
197533 TAAAATATTATGCACA
1 TAAAATA-TATG-ACA
* *
197549 TAAAATAAAT-ATA
1 TAAAATATATGACA
197562 TAAAATATATGA-A
1 TAAAATATATGACA
197575 TAAAATATA
1 TAAAATATA
197584 AATCTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 21 0.68
14 1 0.03
15 2 0.06
16 7 0.23
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (14 bp):
TAAAATATATGACA
Found at i:197585 original size:28 final size:33
Alignment explanation
Indices: 197513--197586 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 33
197503 TAAATATAAT
197513 ATAAAATATAAAATAATATTTAAAATATTATGCAC
1 ATAAAATAT-AAATAATA-TTAAAATATTATGCAC
197548 AT-AAA-ATAAAT-ATA-TAAAATA-TATG-A-
1 ATAAAATATAAATAATATTAAAATATTATGCAC
197574 ATAAAATATAAAT
1 ATAAAATATAAAT
197587 CTATTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 10 0.27
29 7 0.19
31 3 0.08
32 4 0.11
33 2 0.05
34 3 0.08
35 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAAAATATAAATAATATTAAAATATTATGCAC
Found at i:197595 original size:19 final size:21
Alignment explanation
Indices: 197552--197598 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
197542 ATGCACATAA
197552 AATAAATATATAAAATATATG
1 AATAAATATATAAAATATATG
* *
197573 AATAAA-ATAT-AAATCTATT
1 AATAAATATATAAAATATATG
197592 AATAAAT
1 AATAAAT
197599 TAATGGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAAATATATAAAATATATG
Found at i:198123 original size:8 final size:9
Alignment explanation
Indices: 198106--198191 Score: 52
Period size: 9 Copynumber: 9.3 Consensus size: 9
198096 AAAATCTTAA
198106 ATTTTATAT
1 ATTTTATAT
198115 ATTTT-TAT
1 ATTTTATAT
*
198123 ATTATA-AT
1 ATTTTATAT
* * *
198131 CATGTAAAAT
1 -ATTTTATAT
198141 ATTTATATAT
1 ATTT-TATAT
*
198151 ATTTATATTAA
1 ATTT-TA-TAT
198162 ATATTTATAT
1 AT-TTTATAT
*
198172 A-ATTATAT
1 ATTTTATAT
198180 ATTTTATAT
1 ATTTTATAT
198189 ATT
1 ATT
198192 ATAAAATATT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
8 16 0.27
9 20 0.34
10 15 0.25
11 6 0.10
12 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
ATTTTATAT
Found at i:198148 original size:34 final size:32
Alignment explanation
Indices: 198104--198195 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 32
198094 ATAAAATCTT
198104 AAAT-TTTATATATTTTTATATTATAATCATGTA
1 AAATATTTATATATTTTTATATTATAAT-AT-TA
* *
198137 AAATATTTATATATATTTATATTA-AATATTT
1 AAATATTTATATATTTTTATATTATAATATTA
* *
198168 ATATAATTATATATTTTATATATTATAA
1 AAATATTTATATATTTT-TATATTATAA
198196 AATATTTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 15 0.29
32 9 0.18
33 9 0.18
34 18 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
AAATATTTATATATTTTTATATTATAATATTA
Found at i:198176 original size:16 final size:17
Alignment explanation
Indices: 198157--198204 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
198147 ATATATTTAT
198157 ATTAAATA-TTTATATA
1 ATTAAATATTTTATATA
*
198173 ATTATATATTTTATATA
1 ATTAAATATTTTATATA
*
198190 TTATAAAATATTTTA
1 --ATTAAATATTTTA
198205 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
19 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAAATATTTTATATA
Found at i:198188 original size:23 final size:23
Alignment explanation
Indices: 198137--198182 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
198127 TAATCATGTA
198137 AAATATTTATATATATTTATATT
1 AAATATTTATATATATTTATATT
198160 AAATATTTATATA-ATTATATATT
1 AAATATTTATATATATT-TATATT
198183 TTATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AAATATTTATATATATTTATATT
Found at i:200500 original size:7 final size:7
Alignment explanation
Indices: 200483--200516 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
200473 TTGCTCCTTT
200483 TAAAGAAA
1 TAAA-AAA
200491 TAAAAAA
1 TAAAAAA
200498 TAAAAAA
1 TAAAAAA
200505 TAAAAAA
1 TAAAAAA
200512 TAAAA
1 TAAAA
200517 TCCTACGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:202404 original size:5 final size:5
Alignment explanation
Indices: 202394--202425 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
202384 ATATATAATC
202394 AAATT AAATT -AATT AAATT AAATT -AATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAAT
202426 CAATTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AAATT
Found at i:202411 original size:14 final size:14
Alignment explanation
Indices: 202389--202425 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
202379 TAAAAATATA
*
202389 TAATCAAATTAAAT
1 TAATTAAATTAAAT
202403 TAATTAAATTAAAT
1 TAATTAAATTAAAT
202417 TAATTAAAT
1 TAATTAAAT
202426 CAATTAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTAAATTAAAT
Found at i:202937 original size:19 final size:20
Alignment explanation
Indices: 202900--202942 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
202890 TGATTAGTTA
202900 TAAAAAATTAATTTAAATAT
1 TAAAAAATTAATTTAAATAT
202920 TAAAAAATTAATTT-AATAT
1 TAAAAAATTAATTTAAATAT
202939 TAAA
1 TAAA
202943 TATAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAATTAATTTAAATAT
Found at i:204342 original size:16 final size:18
Alignment explanation
Indices: 204309--204355 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
204299 TTTAATTTTT
*
204309 TAATTTTATGTTAAAAATA
1 TAATTTTAT-TAAAAAATA
204328 T-ATTTT-TTAAAAAATA
1 TAATTTTATTAAAAAATA
204344 TAATTTTATTAA
1 TAATTTTATTAA
204356 TTATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 9 0.36
19 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATTTTATTAAAAAATA
Found at i:204689 original size:10 final size:12
Alignment explanation
Indices: 204666--204702 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
204656 TTAATTATAA
204666 AATA-TATAAAT
1 AATATTATAAAT
204677 AATATT-T-AAT
1 AATATTATAAAT
204687 AATATTATAAAT
1 AATATTATAAAT
204699 AATA
1 AATA
204703 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.39
11 6 0.26
12 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATTATAAAT
Found at i:210420 original size:2 final size:2
Alignment explanation
Indices: 210413--210437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
210403 TGGAGGCATT
210413 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
210438 AATGTCTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:211416 original size:26 final size:25
Alignment explanation
Indices: 211341--211442 Score: 77
Period size: 26 Copynumber: 4.1 Consensus size: 25
211331 ACTCATTAAG
**
211341 TTTTTA-A-ATTTAATTAAGAAGAAT
1 TTTTTATATATTTAATTATTAA-AAT
* **
211365 TTTTTATATTTTCTAA-TATTTTAAT
1 TTTTTATATATT-TAATTATTAAAAT
211390 TTATTTATATATTTAATTATTAAAAT
1 TT-TTTATATATTTAATTATTAAAAT
* *
211416 TTTTAAATATTTTTAATT-TTAAAAT
1 TTTT-TATATATTTAATTATTAAAAT
211441 TT
1 TT
211443 ATATTTACGT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
24 6 0.10
25 20 0.32
26 33 0.53
27 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTTTATATATTTAATTATTAAAAT
Found at i:211951 original size:21 final size:21
Alignment explanation
Indices: 211926--211966 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
211916 TATTTTTATT
211926 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
211947 TAAATATTAATATAAAATAT
1 TAAATATTAATATAAAATAT
211967 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:212451 original size:16 final size:17
Alignment explanation
Indices: 212405--212475 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 17
212395 TTAATATTTC
*
212405 ATATATTTATATTTTATTA
1 ATATA-TTATATTATA-TA
* *
212424 ATTTATTCTATTATATA
1 ATATATTATATTATATA
*
212441 ATA-ATTATATT-TAAA
1 ATATATTATATTATATA
*
212456 ATATTTTATATTTATATA
1 ATATATTATA-TTATATA
212474 AT
1 AT
212476 TTTTATTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
15 6 0.15
16 12 0.29
17 6 0.15
18 13 0.32
19 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTATATTATATA
Found at i:212484 original size:15 final size:14
Alignment explanation
Indices: 212434--212494 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 14
212424 ATTTATTCTA
*
212434 TTATATAATAA-TT
1 TTATTTAATAATTT
* *
212447 ATATTTAAAATATTT
1 TTATTTAATA-ATTT
212462 TATATTTATATAATTT
1 T-TATTTA-ATAATTT
*
212478 TTATTTAATAAATT
1 TTATTTAATAATTT
212492 TTA
1 TTA
212495 AAAAATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
13 7 0.18
14 10 0.26
15 8 0.21
16 11 0.29
17 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTTAATAATTT
Found at i:212533 original size:41 final size:43
Alignment explanation
Indices: 212453--212535 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
212443 AATTATATTT
* *
212453 AAAATATTTTATATTTATATAATTTTTATTTAATAAATTTTAA
1 AAAATATTTTATATTTATATAATTTATATTCAATAAATTTTAA
*
212496 AAAATATTTTATATATT-TAT-A-TTATATTCATATAATTTTT
1 AAAATATTTTATAT-TTATATAATTTATATTCA-ATAAATTTT
212536 TATATTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 7 0.20
42 9 0.26
43 17 0.49
44 2 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (43 bp):
AAAATATTTTATATTTATATAATTTATATTCAATAAATTTTAA
Found at i:212778 original size:3 final size:3
Alignment explanation
Indices: 212770--212798 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
212760 CTATGATGCA
212770 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
212799 CCTCAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:219251 original size:20 final size:22
Alignment explanation
Indices: 219207--219252 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
219197 TTTAAGTAAT
* *
219207 TAATTTAAATTTAAATTTAATA
1 TAATTTAAATTTAAATTAAAAA
219229 TAATTT-AA-TTAAATTAAAAA
1 TAATTTAAATTTAAATTAAAAA
219249 TAAT
1 TAAT
219253 AGTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTTAAATTTAAATTAAAAA
Found at i:219294 original size:43 final size:41
Alignment explanation
Indices: 219217--219374 Score: 111
Period size: 40 Copynumber: 3.9 Consensus size: 41
219207 TAATTTAAAT
*
219217 TTAAATTTAATATAATTT-AA-TTAAATTAA---AAATAATA
1 TTAAATTTAAT-TAATTTAAATTTAAAATAATTTAAATAATA
*
219254 GTTTAAAATTAATTAATTTAAATTTAAAATAATTTAAATAATTAA
1 --TTAAATTTAATTAATTTAAATTTAAAATAATTTAAATAA-T-A
* *
219299 CTTGAATTTAA-TAA-TT-AATATTAAATATAA-TTAAA-ACTA
1 -TTAAATTTAATTAATTTAAAT-TTAAA-ATAATTTAAATAATA
* * *
219338 TTAAATTTAATTAATATAAATTTAAATTGATTTAAAT
1 TTAAATTTAATTAATTTAAATTTAAAATAATTTAAAT
219375 TTAATTATGT
Statistics
Matches: 95, Mismatches: 10, Indels: 26
0.73 0.08 0.20
Matches are distributed among these distances:
38 15 0.16
39 18 0.19
40 20 0.21
41 7 0.07
42 12 0.13
43 13 0.14
44 9 0.09
45 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (41 bp):
TTAAATTTAATTAATTTAAATTTAAAATAATTTAAATAATA
Found at i:219295 original size:29 final size:28
Alignment explanation
Indices: 219203--219333 Score: 88
Period size: 29 Copynumber: 4.3 Consensus size: 28
219193 AATTTTTAAG
*
219203 TAATT-AATTTAAATTTAAATTTAATATAATT
1 TAATTAAATTTAAA-AT-AATTTAA-ATAA-T
*
219234 TAATTAAATTAAAAATAATAGTTTAAAATTAAT
1 TAATTAAATTTAAAAT-A-A-TTT-AAA-TAAT
219267 TAATTTAAATTTAAAATAATTTAAATAAT
1 TAA-TTAAATTTAAAATAATTTAAATAAT
*
219296 TAACTTGAATTTAATAATTAATATTAAAT-A-
1 TAA-TTAAATTTAA-AA-TAAT-TTAAATAAT
219326 TAATTAAA
1 TAATTAAA
219334 ACTATTAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
29 20 0.24
30 8 0.09
31 16 0.19
32 15 0.18
33 9 0.11
34 17 0.20
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATTAAATTTAAAATAATTTAAATAAT
Found at i:219387 original size:15 final size:15
Alignment explanation
Indices: 219203--219414 Score: 119
Period size: 16 Copynumber: 13.2 Consensus size: 15
219193 AATTTTTAAG
219203 TAATTAATTTAAATT
1 TAATTAATTTAAATT
*
219218 TAAATTTAATAT-AATT
1 T-AA-TTAATTTAAATT
* **
219234 TAATTAAATTAAAAA
1 TAATTAATTTAAATT
* *
219249 TAA-TAGTTTAAAAT
1 TAATTAATTTAAATT
219263 TAATTAATTTAAATT
1 TAATTAATTTAAATT
*
219278 TAAAATAATTTAAATAAT
1 T-AATTAATTTAAAT--T
219296 TAACTTGAATTT-AA--
1 TAA-TT-AATTTAAATT
*
219310 TAATTAATATTAAATA
1 TAATTAAT-TTAAATT
219326 TAATTAAAACTATTAAATT
1 TAATT--AA-T-TTAAATT
*
219345 TAATTAATATAAATT
1 TAATTAATTTAAATT
*
219360 TAAATTGATTTAAATT
1 T-AATTAATTTAAATT
219376 TAATTATGTTAATATTAAATT
1 T-A--A--TTAAT-TTAAATT
*
219397 TAATTAATTTAAAAT
1 TAATTAATTTAAATT
219412 TAA
1 TAA
219415 AATTATTAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
12 3 0.02
13 4 0.03
14 21 0.13
15 34 0.22
16 45 0.29
17 10 0.06
18 9 0.06
19 18 0.11
20 5 0.03
21 8 0.05
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (15 bp):
TAATTAATTTAAATT
Found at i:219393 original size:21 final size:21
Alignment explanation
Indices: 219369--219445 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
219359 TTAAATTGAT
*
219369 TTAAATTTAATT-ATGTTAATA
1 TTAAATTTAATTAAT-TTAAAA
219390 TTAAATTTAATTAATTTAAAA
1 TTAAATTTAATTAATTTAAAA
*
219411 TTAAAATT-ATTAAATTTAAAA
1 TTAAATTTAATT-AATTTAAAA
*
219432 -TAATTTTAAATTAA
1 TTAAATTT-AATTAA
219446 AATTATATCT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.17
21 35 0.73
22 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TTAAATTTAATTAATTTAAAA
Found at i:219413 original size:82 final size:81
Alignment explanation
Indices: 219228--219429 Score: 205
Period size: 82 Copynumber: 2.5 Consensus size: 81
219218 TAAATTTAAT
* * * * *
219228 ATAATTTAATTAAATTAAAAATAATAGT-TTAAAATTAATTAATTTAAATTTAAAATAATTTAAA
1 ATAATTTAATT-AATTAAAATTAAAACTATTAAATTTAATTAATATAAATTTAAAATAATTTAAA
219292 TAATTAACTTGAATTTA
65 TAATTAACTTGAATTTA
* * * * *
219309 ATAATTAATATTAAATATAATTAAAACTATTAAATTTAATTAATATAAATTTAAATTGATTTAAA
1 ATAATTTA-ATTAATTAAAATTAAAACTATTAAATTTAATTAATATAAATTTAAAATAATTTAAA
**
219374 TTTAATTATGTT-AATATT-
65 --TAATTAACTTGAAT-TTA
*
219392 A-AATTTAATTAATTTAAAATTAAAATTATTAAATTTAA
1 ATAATTTAATTAA-TTAAAATTAAAACTATTAAATTTAA
219430 AATAATTTTA
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
81 23 0.23
82 62 0.63
83 4 0.04
84 10 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (81 bp):
ATAATTTAATTAATTAAAATTAAAACTATTAAATTTAATTAATATAAATTTAAAATAATTTAAAT
AATTAACTTGAATTTA
Found at i:219423 original size:15 final size:15
Alignment explanation
Indices: 219405--219451 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
219395 TTTAATTAAT
219405 TTAAAATTAAAATTA
1 TTAAAATTAAAATTA
* *
219420 TTAAATTTAAAATAA
1 TTAAAATTAAAATTA
*
219435 TTTTAAATTAAAATTA
1 -TTAAAATTAAAATTA
219451 T
1 T
219452 ATCTCATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAATTAAAATTA
Found at i:219430 original size:36 final size:35
Alignment explanation
Indices: 219337--219430 Score: 84
Period size: 36 Copynumber: 2.6 Consensus size: 35
219327 AATTAAAACT
* * *
219337 ATTAAATTTAATTAATATAAATTTAAATTGATTTAA
1 ATTAAAATT-ATTAATTTAAATTTAAATTAATTTAA
*
219373 ATT-TAATTATGTTAATATTAAATTT-AATTAATTTAAA
1 ATTAAAATTA--TTAAT-TTAAATTTAAATTAATTT-AA
219410 ATTAAAATTATTAAATTTAAA
1 ATTAAAATTATT-AATTTAAA
219431 ATAATTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
34 1 0.02
35 3 0.06
36 23 0.49
37 15 0.32
38 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (35 bp):
ATTAAAATTATTAATTTAAATTTAAATTAATTTAA
Found at i:219443 original size:31 final size:30
Alignment explanation
Indices: 219388--219451 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
219378 ATTATGTTAA
*
219388 TATTAAATTTAATTAATTTAAAATTAAAAT
1 TATTAAATTTAAATAATTTAAAATTAAAAT
*
219418 TATTAAATTTAAAATAATTTTAAATTAAAAT
1 TATTAAATTT-AAATAATTTAAAATTAAAAT
219449 TAT
1 TAT
219452 ATCTCATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTAAATTTAAATAATTTAAAATTAAAAT
Found at i:219445 original size:52 final size:52
Alignment explanation
Indices: 219336--219446 Score: 138
Period size: 52 Copynumber: 2.1 Consensus size: 52
219326 TAATTAAAAC
* *
219336 TATTAAATTTAATTAATATAAATTTAAATTGATTTAAATTTAATTATGTTAA
1 TATTAAATTTAATTAATATAAATTAAAATTGATTTAAATTTAATAATGTTAA
* *
219388 TATTAAATTTAATTAATTTAAAATTAAAATT-A-TTAAATTTAAAATAATTTTAA
1 TATTAAATTTAATTAATAT-AAATTAAAATTGATTTAAATTT--AATAATGTTAA
219441 -ATTAAA
1 TATTAAA
219447 ATTATATCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
51 8 0.15
52 25 0.48
53 19 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (52 bp):
TATTAAATTTAATTAATATAAATTAAAATTGATTTAAATTTAATAATGTTAA
Found at i:219447 original size:16 final size:16
Alignment explanation
Indices: 219385--219453 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
219375 TTAATTATGT
* *
219385 TAATATTAAATTTAAT
1 TAATATTAAATTAAAA
219401 TAAT-TTAAAATTAAAA
1 TAATATT-AAATTAAAA
219417 T--TATTAAATTTAAAA
1 TAATATTAAA-TTAAAA
*
219432 TAATTTTAAATTAAAA
1 TAATATTAAATTAAAA
*
219448 TTATAT
1 TAATAT
219454 CTCATTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.09
15 11 0.26
16 22 0.51
17 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATATTAAATTAAAA
Found at i:220922 original size:19 final size:19
Alignment explanation
Indices: 220879--220923 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
220869 AATCAAACAG
220879 ATTTAAAATAATAATTTTA
1 ATTTAAAATAATAATTTTA
* *
220898 AATTAAAA-AATATATTTTT
1 ATTTAAAATAATA-ATTTTA
220917 ATTTAAA
1 ATTTAAA
220924 TTTAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAAATAATAATTTTA
Found at i:233389 original size:17 final size:17
Alignment explanation
Indices: 233341--233402 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
233331 TTTTTAAATT
*
233341 TTAAAAAATTTTAAGTTTAA
1 TTAAAATATTTT-A-TTT-A
233361 TTAAAATATTTTATTTA
1 TTAAAATATTTTATTTA
233378 TTAATAAT-TTTTATTAATA
1 TTAA-AATATTTTATT--TA
233397 TTAAAA
1 TTAAAA
233403 GTTATATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 12 0.32
18 8 0.21
19 7 0.18
20 11 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAAAATATTTTATTTA
Found at i:235145 original size:22 final size:21
Alignment explanation
Indices: 235117--235169 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 21
235107 ATAAATACTT
235117 AATATAAATTAATATTTCATTTG
1 AATATAAATTAA-ATTT-ATTTG
235140 AA-AT-AA--AAATTTATTTG
1 AATATAAATTAAATTTATTTG
235157 AATATAAATTAAA
1 AATATAAATTAAA
235170 AAATAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 4 0.15
21 5 0.19
22 2 0.08
23 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AATATAAATTAAATTTATTTG
Found at i:235170 original size:22 final size:23
Alignment explanation
Indices: 235117--235170 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 23
235107 ATAAATACTT
*
235117 AATATAAATTAATATTTCATTTG
1 AATATAAATTAAAATTTCATTTG
235140 AA-AT--A--AAAATTT-ATTTG
1 AATATAAATTAAAATTTCATTTG
235157 AATATAAATTAAAA
1 AATATAAATTAAAA
235171 AATAAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 11
0.68 0.03 0.30
Matches are distributed among these distances:
17 7 0.28
18 8 0.32
20 2 0.08
22 6 0.24
23 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
AATATAAATTAAAATTTCATTTG
Found at i:237044 original size:5 final size:5
Alignment explanation
Indices: 237018--237082 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
237008 ACTTATCAAT
**
237018 TTTAA TTTAAA TTTAA -AAAA TTTAA -TTAA -TTAA TTTATA TTTAAA
1 TTTAA TTT-AA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA-A TTT-AA
237063 TTTAA TTTAA -TTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA T
237083 AAAAAATTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 14 0.28
5 22 0.44
6 13 0.26
7 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:237089 original size:26 final size:25
Alignment explanation
Indices: 237018--237096 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 25
237008 ACTTATCAAT
*
237018 TTTAATTTAAATT-TAAAAAATTTAA
1 TTTAA-TTAATTTATAAAAAATTTAA
**
237043 -TTAATTAATTTATATTTAAATTTAA
1 TTTAATTAATTTATA-AAAAATTTAA
237068 TTTAATTAATTTAATAAAAAATTTGAA
1 TTTAATTAATTT-ATAAAAAATTT-AA
237095 TT
1 TT
237097 AAAATTGACT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 6 0.14
24 6 0.14
25 8 0.18
26 17 0.39
27 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTAATTAATTTATAAAAAATTTAA
Found at i:237098 original size:26 final size:24
Alignment explanation
Indices: 237031--237098 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 24
237021 AATTTAAATT
237031 TAAAAAATTTAATTAATTAATTTA
1 TAAAAAATTTAATTAATTAATTTA
**
237055 TATTTAAATTTAATTTAATTAATTTAA
1 TA-AAAAATTTAA-TTAATTAATTT-A
237082 TAAAAAATTTGAATTAA
1 TAAAAAATTT-AATTAA
237099 AATTGACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 2 0.06
25 8 0.22
26 21 0.58
27 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
TAAAAAATTTAATTAATTAATTTA
Found at i:237266 original size:16 final size:16
Alignment explanation
Indices: 237243--237284 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
237233 TAATTAATTC
237243 AAATTTAAAATTAAAA
1 AAATTTAAAATTAAAA
** *
237259 TTATTTAAATTTAAAA
1 AAATTTAAAATTAAAA
237275 AAATTTAAAA
1 AAATTTAAAA
237285 ATGTAATTCA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAAAATTAAAA
Found at i:237747 original size:24 final size:24
Alignment explanation
Indices: 237672--237779 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
237662 TTGATAAGTT
*
237672 TAAATATAATAT-AATTATACAATA
1 TAAATATAATATAAATTAT-TAATA
* * *
237696 AAAATAT-ATA-AAAATATTAAAA
1 TAAATATAATATAAATTATTAATA
**
237718 TTTATATAATATAAATTATTAATA
1 TAAATATAATATAAATTATTAATA
* *
237742 TATATA-AATATATAATTTTTAAATA
1 TAAATATAATATA-AATTATT-AATA
237767 TAAATATAATATA
1 TAAATATAATATA
237780 TAAAAATATA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
22 7 0.11
23 17 0.26
24 27 0.41
25 9 0.14
26 6 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATATAATATAAATTATTAATA
Found at i:237769 original size:21 final size:21
Alignment explanation
Indices: 237707--237809 Score: 74
Period size: 21 Copynumber: 5.0 Consensus size: 21
237697 AAATATATAA
*
237707 AAATATTAAAATTTATATAATAT
1 AAATA-TATAATTTATA-AATAT
237730 AAAT-TATTAA--TAT--ATAT
1 AAATATA-TAATTTATAAATAT
*
237747 AAATATATAATTTTTAAATAT
1 AAATATATAATTTATAAATAT
* *
237768 AAATATA-ATATATAAAAATAT
1 AAATATATA-ATTTATAAATAT
*
237789 AAAAATATAATATTATAAATA
1 AAATATATAAT-TTATAAATA
237810 ATTGGATGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
17 11 0.17
18 2 0.03
19 2 0.03
20 4 0.06
21 30 0.48
22 10 0.16
23 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATATAATTTATAAATAT
Found at i:237979 original size:69 final size:70
Alignment explanation
Indices: 237893--238026 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 70
237883 AACAAAATCT
*
237893 TTTAGGCCTATTTTGAC-TAGAGGCAAATATTTTCT-GTAGAGTGTCTTTTCAAGC-TTTTTGCT
1 TTTAGGCCTATTTTGACTTAG-GGCAAATATTTTCTCG-AGAGTGTCTTGTCAAGCTTTTTTGCT
237955 GGTTACC
64 GGTTACC
* * *
237962 TTTAGGCCTATTTTGACTTTGGGCAAATTTTTTCTCGAGAGTGTCTTGTCGAGCTTTTTTGCTGG
1 TTTAGGCCTATTTTGACTTAGGGCAAATATTTTCTCGAGAGTGTCTTGTCAAGCTTTTTTGCTGG
238027 GTTTTTTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
69 45 0.78
70 13 0.22
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (70 bp):
TTTAGGCCTATTTTGACTTAGGGCAAATATTTTCTCGAGAGTGTCTTGTCAAGCTTTTTTGCTGG
TTACC
Found at i:239236 original size:11 final size:11
Alignment explanation
Indices: 239222--239247 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
239212 TAAATTAAAA
239222 TTTTAATTTAT
1 TTTTAATTTAT
239233 TTTTAATTTAT
1 TTTTAATTTAT
239244 TTTT
1 TTTT
239248 GTTATACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTAATTTAT
Found at i:239857 original size:24 final size:23
Alignment explanation
Indices: 239830--239886 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
239820 TATTTGAAGT
**
239830 TATATTTTAATATTTATATTTAAA
1 TATATTTTAATATGAATATTT-AA
239854 TATATTTTTAATATGAATATTTAA
1 TATA-TTTTAATATGAATATTTAA
239878 TA-ATTTTAA
1 TATATTTTAA
239887 AAATTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 6 0.20
23 1 0.03
24 8 0.27
25 15 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATTTTAATATGAATATTTAA
Found at i:240271 original size:21 final size:22
Alignment explanation
Indices: 240229--240271 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
240219 ATAAAAATAT
**
240229 ATTTTTAATGAAATTATTTAAA
1 ATTTTTAATGAAATTAAATAAA
*
240251 ATTTTTTAT-AAATTAAATAAA
1 ATTTTTAATGAAATTAAATAAA
240272 TATATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTTTAATGAAATTAAATAAA
Found at i:241637 original size:2 final size:2
Alignment explanation
Indices: 241630--241659 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
241620 AAAGCACCAC
241630 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
241660 TGTATAGTCA
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):
AT
Found at i:242013 original size:14 final size:14
Alignment explanation
Indices: 241994--242021 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
241984 TTTAAGATAA
241994 TTAAATATATATTT
1 TTAAATATATATTT
242008 TTAAATATATATTT
1 TTAAATATATATTT
242022 ATATCTAATA
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):
TTAAATATATATTT
Found at i:264832 original size:14 final size:14
Alignment explanation
Indices: 264813--264839 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
264803 CTTTTAAATA
264813 TAATAAAAGTAATG
1 TAATAAAAGTAATG
264827 TAATAAAAGTAAT
1 TAATAAAAGTAAT
264840 ACATTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
TAATAAAAGTAATG
Found at i:264949 original size:16 final size:16
Alignment explanation
Indices: 264928--264959 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
264918 ATTTTAAAAA
264928 TAAATTAATTAATTTT
1 TAAATTAATTAATTTT
*
264944 TAAATTAATTTATTTT
1 TAAATTAATTAATTTT
264960 ATATTTTTCA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTAATTAATTTT
Found at i:265003 original size:43 final size:43
Alignment explanation
Indices: 264946--265076 Score: 124
Period size: 43 Copynumber: 3.0 Consensus size: 43
264936 TTAATTTTTA
*
264946 AATTAATTTATTTTATATTTTTCATAAGTTTGTAAAAATTGTG
1 AATTAATTTATTTTATATTTTTCATAAGTTTATAAAAATTGTG
* * * ** * *
264989 AATTAATTT-TTTT-TAATTTT-AGAAATGAATAAATTAATTTTTA
1 AATTAATTTATTTTATATTTTTCATAAGTTTATAAA--AA-TTGTG
* *
265032 AATTAATTTGTTTTATATTTTTCATAAGTTTCTAAAAATTGTG
1 AATTAATTTATTTTATATTTTTCATAAGTTTATAAAAATTGTG
265075 AA
1 AA
265077 GGTGTTGTTT
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
40 8 0.12
41 6 0.09
42 6 0.09
43 26 0.39
44 6 0.09
45 6 0.09
46 8 0.12
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (43 bp):
AATTAATTTATTTTATATTTTTCATAAGTTTATAAAAATTGTG
Found at i:265024 original size:86 final size:85
Alignment explanation
Indices: 264912--265076 Score: 276
Period size: 86 Copynumber: 1.9 Consensus size: 85
264902 TATCAGTTAA
*
264912 TTTTTTATTTTAAAAATAAATTAATTAATTTTTAAATTAATTTATTTTATATTTTTCATAAGTTT
1 TTTTTTATTTTAAAAATAAATAAATTAATTTTTAAATTAATTTATTTTATATTTTTCATAAGTTT
*
264977 GTAAAAATTGTGAATTAATT
66 CTAAAAATTGTGAATTAATT
* * *
264997 TTTTTTAATTTTAGAAATGAATAAATTAATTTTTAAATTAATTTGTTTTATATTTTTCATAAGTT
1 TTTTTT-ATTTTAAAAATAAATAAATTAATTTTTAAATTAATTTATTTTATATTTTTCATAAGTT
265062 TCTAAAAATTGTGAA
65 TCTAAAAATTGTGAA
265077 GGTGTTGTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 6 0.08
86 68 0.92
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (85 bp):
TTTTTTATTTTAAAAATAAATAAATTAATTTTTAAATTAATTTATTTTATATTTTTCATAAGTTT
CTAAAAATTGTGAATTAATT
Found at i:265393 original size:26 final size:29
Alignment explanation
Indices: 265346--265400 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 29
265336 TTTAATTAAA
*
265346 TTTAATATAATTAAATTATTAAAATATTT
1 TTTAATATAATTAAAATATTAAAATATTT
*
265375 TTTAA-ATAA-TAAAAT-TTAATATATTT
1 TTTAATATAATTAAAATATTAAAATATTT
265401 ATAATCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 5 0.21
28 4 0.17
29 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAATATAATTAAAATATTAAAATATTT
Found at i:269377 original size:13 final size:13
Alignment explanation
Indices: 269359--269391 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
269349 TTTTTAAATA
269359 AATATTTATATTT
1 AATATTTATATTT
*
269372 AATATTTATTTTT
1 AATATTTATATTT
269385 AA-ATTTA
1 AATATTTA
269392 AATAACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:272411 original size:2 final size:2
Alignment explanation
Indices: 272404--272438 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
272394 ACTTATTTCA
272404 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 A
272439 ACCCTCTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:273611 original size:12 final size:12
Alignment explanation
Indices: 273596--273646 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
273586 TTGTTCATAT
*
273596 TTTTATATTGTA
1 TTTTATATTATA
*
273608 TTTTA-ATTATTT
1 TTTTATATTA-TA
273620 TTTTATATTATA
1 TTTTATATTATA
273632 TTTTATATTATA
1 TTTTATATTATA
273644 TTT
1 TTT
273647 GAATCAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.09
12 27 0.79
13 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:273622 original size:24 final size:25
Alignment explanation
Indices: 273595--273642 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
273585 TTTGTTCATA
*
273595 TTTTTATATTGTATTTTA-ATTATT
1 TTTTTATATTATATTTTATATTATT
273619 TTTTTATATTATATTTTATATTAT
1 TTTTTATATTATATTTTATATTAT
273643 ATTTGAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTTATATTATATTTTATATTATT
Found at i:273930 original size:23 final size:22
Alignment explanation
Indices: 273877--273935 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
273867 CATATCGTAC
*
273877 TTTAATTTAAATCATAAATTAT
1 TTTAATTTAAATAATAAATTAT
* * *
273899 TTAATATTTATATAATAATTTAAT
1 TTTA-ATTTAAATAATAAATT-AT
273923 TTTAATTTTAAAT
1 TTTAA-TTTAAAT
273936 TTATTTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 3 0.11
23 14 0.50
24 11 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATTTAAATAATAAATTAT
Found at i:273972 original size:19 final size:19
Alignment explanation
Indices: 273957--273995 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
273947 AAATAAAAAT
273957 ATAAAAATTATTTAAATAA
1 ATAAAAATTATTTAAATAA
*
273976 ATAATAATTATTTAATATAA
1 ATAAAAATTATTTAA-ATAA
273996 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAAATTATTTAAATAA
Found at i:274024 original size:26 final size:27
Alignment explanation
Indices: 273993--274044 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
273983 TTATTTAATA
* * *
273993 TAATTTAATTTAAA-TTATATATATTT
1 TAATTTAACTAAAATTTATAAATATTT
274019 TAATTTAACTAAAATTTATAAATATT
1 TAATTTAACTAAAATTTATAAATATT
274045 ATGAATGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATTTAACTAAAATTTATAAATATTT
Found at i:276226 original size:113 final size:113
Alignment explanation
Indices: 276028--276244 Score: 355
Period size: 113 Copynumber: 1.9 Consensus size: 113
276018 ATGAACCAAC
* * *
276028 GAGACACAACGTGCTTTAGTCACCTTCCTTCTTGACAATGACATCCCATGTCTACTTGCCTTAAA
1 GAGACACAACATGCTTTAGTCACCTTCCTTCTGGACAATGACAACCCATGTCTACTTGCCTTAAA
* *
276093 ATCCAGTTCCTGTCTTCATAACATCAATGGCAAGTAGTTGGAAACAAA
66 ATCCAGTTCCTGTCTACATAACATCAATGGCAAATAGTTGGAAACAAA
* *
276141 GAGACACAACATGCTTTAGTCACCTTCCTTCTGGGGCAATGACAACCCATGT-TACTTGCCTTGA
1 GAGACACAACATGCTTTAGTCACCTTCCTTCT-GGACAATGACAACCCATGTCTACTTGCCTTAA
276205 AATCCAGTTCCTGTCTACATAACATCAATGGCAAATAGTT
65 AATCCAGTTCCTGTCTACATAACATCAATGGCAAATAGTT
276245 AGCGAACTTC
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 80 0.83
114 16 0.17
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (113 bp):
GAGACACAACATGCTTTAGTCACCTTCCTTCTGGACAATGACAACCCATGTCTACTTGCCTTAAA
ATCCAGTTCCTGTCTACATAACATCAATGGCAAATAGTTGGAAACAAA
Found at i:281279 original size:108 final size:111
Alignment explanation
Indices: 281061--281727 Score: 717
Period size: 112 Copynumber: 6.0 Consensus size: 111
281051 AGTCTCGTAG
* * ** * ** *
281061 CCTGTTTGTCGATGTCTGCATTCTCATATCCGGGCTTCAACTATACAGTCCCGACCCAATTTGTC
1 CCTGTTTGTCTATGTCGGCA-AGTCATATCTGGGCTTCAACTATACAGTCCCGACCCAATCCGCC
* *
281126 TCAACCTAGTCATCCAGGAAATTTAACATTTCCATACTTCCTTCCTT
65 TCAACTTAGTCATCCAGGAAATTTAACATATCCATACTTCCTTCCTT
* * *
281173 CCTGTTTGTCTATCTCGGCAA-TC-T-T-TGGGGCTTCCACTAAACAGTCCCGACCCAATCCGCC
1 CCTGTTTGTCTATGTCGGCAAGTCATATCT-GGGCTTCAACTATACAGTCCCGACCCAATCCGCC
* *
281234 TCAACTTAGTCATCCAGGAAATTTAACACATCTATACCTCCTTCCTTCCTT
65 TCAACTTAGTCATCCAGGAAATTTAACATATCCATA----CTTCCTTCCTT
* ** * * * * * *
281285 CCTGTTTGTCTATGTAGATAA-TCTTATATCCGGGCTTCAGCTAAACTGTTCCGACCCAATCCGT
1 CCTGTTTGTCTATGTCGGCAAGTC--ATATCTGGGCTTCAACTATACAGTCCCGACCCAATCCGC
*
281349 CTCAACTTAGTCACCCAGGAAATTTAACATATCCATACTTCCTTCCTT
64 CTCAACTTAGTCATCCAGGAAATTTAACATATCCATACTTCCTTCCTT
* * * *
281397 CCTGCTTGTCTATGTCAGCAATGTCATATCTGGGCTTCAAGTATGCA-TCCCCGACCCAATCCGC
1 CCTGTTTGTCTATGTCGGCAA-GTCATATCTGGGCTTCAACTATACAGT-CCCGACCCAATCCGC
* *
281461 CTCAACTTTGTCATCCAGGAAATTTAACATATCCATGCTTCCTTCCTT
64 CTCAACTTAGTCATCCAGGAAATTTAACATATCCATACTTCCTTCCTT
* * * *
281509 CCTGTTTGTCTATGTTGGCAATGTCATATCTGGGCTTCAAGTATGCATTCCCGACCCAATCCGCC
1 CCTGTTTGTCTATGTCGGCAA-GTCATATCTGGGCTTCAACTATACAGTCCCGACCCAATCCGCC
* * ** *
281574 TCAACTTGGTCATCCAGGAAATTTAACATATTCGCAGTTCCTTCCTT
65 TCAACTTAGTCATCCAGGAAATTTAACATATCCATACTTCCTTCCTT
* * * * *
281621 CTTGTTTGTTTATGTCAGCAATGTCATATCTGGGCTTCAACTATACATTCCCAACCCAATCCGCC
1 CCTGTTTGTCTATGTCGGCAA-GTCATATCTGGGCTTCAACTATACAGTCCCGACCCAATCCGCC
* * *
281686 TCAACCTAG---T-C-GGAAATTTAACATATTCAGACTTCCTTCCTT
65 TCAACTTAGTCATCCAGGAAATTTAACATATCCATACTTCCTTCCTT
281728 TCCTTTTTTT
Statistics
Matches: 477, Mismatches: 64, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
107 28 0.06
108 63 0.13
109 2 0.00
110 2 0.00
111 1 0.00
112 314 0.66
113 1 0.00
114 2 0.00
115 1 0.00
116 63 0.13
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33
Consensus pattern (111 bp):
CCTGTTTGTCTATGTCGGCAAGTCATATCTGGGCTTCAACTATACAGTCCCGACCCAATCCGCCT
CAACTTAGTCATCCAGGAAATTTAACATATCCATACTTCCTTCCTT
Found at i:287937 original size:37 final size:37
Alignment explanation
Indices: 287882--287956 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
287872 ACTAGTTACA
*
287882 TGAATCAATTGAACTAAATAAATATGGGTAATAAAAT
1 TGAATCAACTGAACTAAATAAATATGGGTAATAAAAT
*
287919 TGAATCAACTGAATTAAATAAATATGGGTAATAAAAT
1 TGAATCAACTGAACTAAATAAATATGGGTAATAAAAT
287956 T
1 T
287957 TCATTTGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (37 bp):
TGAATCAACTGAACTAAATAAATATGGGTAATAAAAT
Found at i:293980 original size:21 final size:21
Alignment explanation
Indices: 293938--294004 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
293928 ATTGTAATAT
*
293938 TTAATTCAAATTTT-ATTAAAA
1 TTAATT-AAATTTTAATTTAAA
293959 TTAATTAAATTTTAATTTAAA
1 TTAATTAAATTTTAATTTAAA
293980 TAATAATTAAGTATATTTAATTTAA
1 T--TAATTAA--AT-TTTAATTTAA
294005 TTTGTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 7 0.18
21 13 0.33
23 7 0.18
25 2 0.05
26 10 0.26
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
TTAATTAAATTTTAATTTAAA
Found at i:294119 original size:15 final size:15
Alignment explanation
Indices: 294094--294135 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
294084 CAGAAAATAT
294094 TTTTGAAATTAAAAAA
1 TTTT-AAATTAAAAAA
*
294110 TTTTAAATTAAAATA
1 TTTTAAATTAAAAAA
294125 TTTTAAATTAA
1 TTTTAAATTAA
294136 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TTTTAAATTAAAAAA
Found at i:294852 original size:13 final size:14
Alignment explanation
Indices: 294836--294868 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
294826 TTTTATAATT
294836 TTTTTAATAT-TAA
1 TTTTTAATATATAA
*
294849 TTTTAAATATATAA
1 TTTTTAATATATAA
294863 TTTTTA
1 TTTTTA
294869 TGAAATACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTAATATATAA
Found at i:295289 original size:16 final size:17
Alignment explanation
Indices: 295268--295302 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
295258 TAATTTATAA
295268 ATATTTTTATTATT-TT
1 ATATTTTTATTATTATT
*
295284 ATATTTTTCTTATTATT
1 ATATTTTTATTATTATT
295301 AT
1 AT
295303 GATAGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATTTTTATTATTATT
Found at i:295635 original size:31 final size:31
Alignment explanation
Indices: 295545--295632 Score: 101
Period size: 30 Copynumber: 2.8 Consensus size: 31
295535 ATTAATTCGG
*
295545 CCCTCAAATATTTATTTTTAT-TAATTTGA-A
1 CCCTTAAATATTTA-TTTTATCTAATTTGAGA
*
295575 CCCTTAAACATTTATATTTATC-AATTTGAGA
1 CCCTTAAATATTTAT-TTTATCTAATTTGAGA
*
295606 CTCTTAAATATTTATTTTCATCTAATT
1 CCCTTAAATATTTATTTT-ATCTAATT
295633 GAGCCATCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.02
30 27 0.55
31 17 0.35
32 4 0.08
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (31 bp):
CCCTTAAATATTTATTTTATCTAATTTGAGA
Found at i:296361 original size:22 final size:21
Alignment explanation
Indices: 296336--296376 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
296326 AAATTAAAAT
296336 TATTTTAAAATTAATATTTATA
1 TATTTTAAAATTAAT-TTTATA
*
296358 TATTTTATAATTAATTTTA
1 TATTTTAAAATTAATTTTA
296377 AATAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTAAAATTAATTTTATA
Found at i:296612 original size:17 final size:17
Alignment explanation
Indices: 296590--296625 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
296580 AAAAAATTAA
296590 ATATATTTATATAAAAT
1 ATATATTTATATAAAAT
*
296607 ATATATTTATATATAAT
1 ATATATTTATATAAAAT
296624 AT
1 AT
296626 TTAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTTATATAAAAT
Found at i:297524 original size:18 final size:19
Alignment explanation
Indices: 297482--297524 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
297472 ATGAAAAAAA
297482 TATATAAATATATTTTTAT
1 TATATAAATATATTTTTAT
* *
297501 TGTATAAATA-ATTTTTTT
1 TATATAAATATATTTTTAT
297519 TATATA
1 TATATA
297525 TTTTACCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATAAATATATTTTTAT
Found at i:302845 original size:26 final size:28
Alignment explanation
Indices: 302790--302845 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
302780 TTTACGTTTG
*
302790 ATTTAAATTATATAAAAATAATTTTTATT
1 ATTTAAA-TATATAAAAATAATTTATATT
*
302819 ATTTAAA-ATATTAAAA-AATTTATATT
1 ATTTAAATATATAAAAATAATTTATATT
302845 A
1 A
302846 ATATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
27 8 0.32
29 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTAAATATATAAAAATAATTTATATT
Found at i:302858 original size:20 final size:19
Alignment explanation
Indices: 302824--302867 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
302814 TTATTATTTA
302824 AAATATTAAAAAATTTATAT
1 AAATATTAAAAAA-TTATAT
* * *
302844 TAATATTTAATAATTATAT
1 AAATATTAAAAAATTATAT
302863 AAATA
1 AAATA
302868 AAAGTAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTAAAAAATTATAT
Found at i:303244 original size:26 final size:26
Alignment explanation
Indices: 303207--303262 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
303197 TATAATTATA
*
303207 TTTAAAATATT-ATATATTTTATAAAT
1 TTTAAAATATTAATA-ATTATATAAAT
303233 TTTAATAA-ATTAATAATTATATAAAT
1 TTTAA-AATATTAATAATTATATAAAT
303259 TTTA
1 TTTA
303263 TTTATACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAAAATATTAATAATTATATAAAT
Found at i:304601 original size:17 final size:18
Alignment explanation
Indices: 304569--304622 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
304559 TAATATATAA
304569 AAATTATATAATTAAATT
1 AAATTATATAATTAAATT
*
304587 AAATTAT-TTATTAAATT
1 AAATTATATAATTAAATT
304604 -AA-TA-ATAATTTAAATT
1 AAATTATATAA-TTAAATT
304620 AAA
1 AAA
304623 CTATCAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
17 11 0.35
18 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTATATAATTAAATT
Found at i:305079 original size:15 final size:15
Alignment explanation
Indices: 305059--305091 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
305049 TATAAATATT
305059 AATAAATTTTAAATA
1 AATAAATTTTAAATA
*
305074 AATAAATTTTATATA
1 AATAAATTTTAAATA
305089 AAT
1 AAT
305092 TTAAATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAATTTTAAATA
Found at i:305089 original size:11 final size:11
Alignment explanation
Indices: 305032--305093 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
305022 AAAATATTAT
305032 TTTTATATAAA
1 TTTTATATAAA
*
305043 TTTAATTATAAA
1 TTTTA-TATAAA
*
305055 TATTA-ATAAA
1 TTTTATATAAA
305065 TTTTAAATAAATAAA
1 TTTT--AT--ATAAA
305080 TTTTATATAAA
1 TTTTATATAAA
305091 TTT
1 TTT
305094 AAATAAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 8 0.20
11 12 0.29
12 10 0.24
13 2 0.05
15 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTATATAAA
Found at i:305094 original size:25 final size:25
Alignment explanation
Indices: 305032--305099 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
305022 AAAATATTAT
*
305032 TTTTATATAAATTT-AAT-TATAAA
1 TTTTATATAAATTTAAATAAATAAA
*
305055 TATTA-ATAAATTTTAAATAAATAAA
1 TTTTATATAAA-TTTAAATAAATAAA
305080 TTTTATATAAATTTAAATAA
1 TTTTATATAAATTTAAATAA
305100 GTTTGATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.13
23 7 0.18
24 3 0.08
25 18 0.47
26 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTATATAAATTTAAATAAATAAA
Found at i:305096 original size:21 final size:20
Alignment explanation
Indices: 305072--305125 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
305062 AAATTTTAAA
*
305072 TAAATAAATTTTATATAAATT
1 TAAATAAATTTGAT-TAAATT
* *
305093 TAAATAAGTTTGATTCAATT
1 TAAATAAATTTGATTAAATT
305113 TATGAATAAATTT
1 TA--AATAAATTT
305126 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 8 0.30
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (20 bp):
TAAATAAATTTGATTAAATT
Found at i:306065 original size:14 final size:14
Alignment explanation
Indices: 306046--306104 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
306036 TTATTAAAAA
306046 ATATTAAAATTTTT
1 ATATTAAAATTTTT
* *
306060 ATATTAATATTTAT
1 ATATTAAAATTTTT
*
306074 ATATTTAAA--TTT
1 ATATTAAAATTTTT
*
306086 A-AATAAAATTTTT
1 ATATTAAAATTTTT
306099 -TATTAA
1 ATATTAA
306105 TTAAATAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
11 5 0.15
12 3 0.09
13 7 0.21
14 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTAAAATTTTT
Found at i:306133 original size:15 final size:15
Alignment explanation
Indices: 306081--306150 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
306071 TATATATTTA
306081 AATTTAAATAAAATT
1 AATTTAAATAAAATT
* *
306096 -TTTTATTAATTAAATAAT
1 AATTTA--AA-TAAA-ATT
*
306114 AATTTATATAAAATT
1 AATTTAAATAAAATT
306129 AATTTAAATAAAA--
1 AATTTAAATAAAATT
306142 AATTTAAAT
1 AATTTAAAT
306151 TGAATTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 9 0.20
14 4 0.09
15 14 0.32
16 6 0.14
17 5 0.11
18 2 0.05
19 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAAATAAAATT
Found at i:306156 original size:28 final size:26
Alignment explanation
Indices: 306100--306164 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
306090 AAAATTTTTT
* *
306100 ATTAATTAAATAATAATTTATATAAA
1 ATTAATTAAATAAAAATTTAAATAAA
**
306126 ATTAATTTAAATAAAAAATTTAAATTGA
1 ATTAA-TTAAAT-AAAAATTTAAATAAA
*
306154 ATTTATTAAAT
1 ATTAATTAAAT
306165 TATATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.16
27 12 0.38
28 15 0.47
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATTAAATAAAAATTTAAATAAA
Found at i:306545 original size:2 final size:2
Alignment explanation
Indices: 306538--306567 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
306528 TATGTCTTTA
306538 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
306568 TCTTATAAAT
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):
AT
Found at i:306943 original size:21 final size:21
Alignment explanation
Indices: 306919--306967 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
306909 TAAAAATTTA
* *
306919 AAAATTATTTAAAT-TTAATAT
1 AAAA-TATGTAAATATTAAAAT
306940 AAAATATGTAAATATTAAAAT
1 AAAATATGTAAATATTAAAAT
306961 AAGAATA
1 AA-AATA
306968 ATATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 12 0.50
22 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAATATGTAAATATTAAAAT
Found at i:307366 original size:20 final size:21
Alignment explanation
Indices: 307328--307371 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
307318 ATAACTTTAA
* *
307328 TTACGATTTATATACATAATTC
1 TTACAATTTATATA-ATAAGTC
307350 TTACAATTTATAT-ATAAGTC
1 TTACAATTTATATAATAAGTC
307370 TT
1 TT
307372 CCGTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (21 bp):
TTACAATTTATATAATAAGTC
Found at i:307806 original size:21 final size:19
Alignment explanation
Indices: 307773--307812 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
307763 ATAATAAAAT
*
307773 AATTTTTAATTAATTTAAA
1 AATTTTTAATTAAATTAAA
307792 AATTATTTAACTTAAATTAAA
1 AATT-TTTAA-TTAAATTAAA
307813 CAAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTTAATTAAATTAAA
Found at i:307913 original size:19 final size:19
Alignment explanation
Indices: 307877--307956 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 19
307867 TAAAACAAAT
307877 ATATTATTATTTAAATATTTAA
1 ATATT-TTATTT--ATATTTAA
307899 ATATTTTATTTATATATT--
1 ATATTTTATTTATAT-TTAA
*
307917 ATATTTTATATTATTTTTAA
1 ATATTTTAT-TTATATTTAA
*
307937 TTAATTTTA-TTATATTTAA
1 AT-ATTTTATTTATATTTAA
307956 A
1 A
307957 ATTACCGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
18 11 0.22
19 18 0.37
20 3 0.06
21 12 0.24
22 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTATTTATATTTAA
Found at i:307928 original size:12 final size:12
Alignment explanation
Indices: 307899--307946 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 12
307889 AAATATTTAA
*
307899 ATATTTTATTTAT
1 ATATTATATTT-T
307912 ATATTATATTTT
1 ATATTATATTTT
307924 ATATTAT-TTTT
1 ATATTATATTTT
307935 A-ATTA-ATTTT
1 ATATTATATTTT
307945 AT
1 AT
307947 TATATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.28
11 5 0.16
12 8 0.25
13 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:309552 original size:16 final size:18
Alignment explanation
Indices: 309530--309570 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
309520 TTTAATCTAT
309530 TTAAATTATATT-TTAAA
1 TTAAATTATATTATTAAA
*
309547 -TAAATT-TTTTATTAAA
1 TTAAATTATATTATTAAA
309563 TTAAATTA
1 TTAAATTA
309571 ATTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAATTATATTATTAAA
Found at i:309651 original size:22 final size:19
Alignment explanation
Indices: 309620--309661 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
309610 TTTTTTTATT
309620 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
309641 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
309661 T
1 T
309662 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:309671 original size:51 final size:51
Alignment explanation
Indices: 309609--309706 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
309599 TAATTAATAA
309609 ATTTTTTTA-TTTAAATTTAATTATAAAATATATAAATAT-TAATATAAAAAT
1 ATTTTTTTATTTTAAATTT-ATTATAAAATATATAAATATAT-ATATAAAAAT
** *
309660 ATTTTTTTATTTTTTATTTATTATAAAATATATATATATATATATAA
1 ATTTTTTTATTTTAAATTTATTATAAAATATATAAATATATATATAA
309707 TATTAACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 34 0.81
52 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (51 bp):
ATTTTTTTATTTTAAATTTATTATAAAATATATAAATATATATATAAAAAT
Found at i:310205 original size:2 final size:2
Alignment explanation
Indices: 310198--310232 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
310188 TCAAAGATTC
310198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
310233 TATTTTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.