Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011134.1 Kokia drynarioides strain JFW-HI SEQ_126107, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 426376
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 428 characters in sequence are not A, C, G, or T
Found at i:119 original size:4 final size:4
Alignment explanation
Indices: 112--158 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
102 TTCTTCCTTC
* *
112 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTAT TT-T TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTC
159 ATTTTTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:127 original size:22 final size:22
Alignment explanation
Indices: 93--146 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
83 ACTTTTTTTT
* *
93 TTTCTCTCCTTCTTCC-TTCTTC
1 TTTCTTTCTTTCTTCCTTTC-TC
*
115 TTTCTTTCTTTCTTTCTTTCTC
1 TTTCTTTCTTTCTTCCTTTCTC
137 TTT-TTTCTTT
1 TTTCTTTCTTT
147 ATTTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.25
22 18 0.64
23 3 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCTTTCTTTCTTCCTTTCTC
Found at i:162 original size:12 final size:12
Alignment explanation
Indices: 115--164 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
105 TTCCTTCTTC
115 TTTCTTTC-TTT
1 TTTCTTTCATTT
*
126 CTTTCTTTCTCTTT
1 -TTTCTTTC-ATTT
140 TTTCTTT-ATTT
1 TTTCTTTCATTT
151 TTTCTTTCATTT
1 TTTCTTTCATTT
163 TT
1 TT
165 CGTTGGTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 10 0.29
12 14 0.41
13 7 0.21
14 3 0.09
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTCATTT
Found at i:1232 original size:7 final size:7
Alignment explanation
Indices: 1220--1249 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1210 GGTAGTGCAG
1220 TGGCTAC
1 TGGCTAC
1227 TGGCTAC
1 TGGCTAC
1234 TGGCTAC
1 TGGCTAC
1241 TGGCTAC
1 TGGCTAC
1248 TG
1 TG
1250 CAGGTTAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.27, G:0.30, T:0.30
Consensus pattern (7 bp):
TGGCTAC
Found at i:1663 original size:17 final size:17
Alignment explanation
Indices: 1641--1677 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1631 ATTATTTGAC
1641 AAAAAAAATCAAAAACT
1 AAAAAAAATCAAAAACT
* *
1658 AAAAAAAATGAAAAATT
1 AAAAAAAATCAAAAACT
1675 AAA
1 AAA
1678 TTGAAGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAAAAATCAAAAACT
Found at i:3812 original size:1 final size:1
Alignment explanation
Indices: 3768--3792 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3758 CAGTAAACAC
3768 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3793 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6158 original size:3 final size:3
Alignment explanation
Indices: 6150--6185 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
6140 TTGGATGAAT
* *
6150 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6186 CAATTTGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:6168 original size:12 final size:12
Alignment explanation
Indices: 6151--6189 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
6141 TGGATGAATT
6151 AATAATAATAAC
1 AATAATAATAAC
*
6163 AATAATAATAAT
1 AATAATAATAAC
*
6175 AATAACAATAAC
1 AATAATAATAAC
6187 AAT
1 AAT
6190 TTGACTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:6186 original size:6 final size:6
Alignment explanation
Indices: 6151--6189 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
6141 TGGATGAATT
* * *
6151 AATAAT AATAAC AATAAT AATAAT AATAAC AATAAC AAT
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AAT
6190 TTGACTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (6 bp):
AATAAC
Found at i:11819 original size:23 final size:23
Alignment explanation
Indices: 11788--11868 Score: 112
Period size: 23 Copynumber: 3.5 Consensus size: 23
11778 ATGCTAGCGC
*
11788 GCTTGCTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
11811 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
11834 GCTTACTAGATT-GCACTGT-GTGT
1 GCTTACT-GTTTCGCACT-TCGTGT
11857 GCTTACTGTTTC
1 GCTTACTGTTTC
11869 CCCAACACTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 3 0.06
23 45 0.87
24 4 0.08
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:17601 original size:22 final size:22
Alignment explanation
Indices: 17574--17625 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
17564 CAAATGAATG
*
17574 GAGAGCACCAAGGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
*
17596 GAGAGCACAAATGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
*
17618 AAGAGCAC
1 GAGAGCAC
17626 TTTACGTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (22 bp):
GAGAGCACAAAGGTGCTAAACA
Found at i:37459 original size:23 final size:24
Alignment explanation
Indices: 37432--37488 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
37422 CGTTTGTTTA
37432 ATGTTCACGAACAT-TAATCGAAC
1 ATGTTCACGAACATATAATCGAAC
* *
37455 ATGTTCATGAACATATAATTGAAC
1 ATGTTCACGAACATATAATCGAAC
*
37479 ACGTTCACGA
1 ATGTTCACGA
37489 GCAATGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (24 bp):
ATGTTCACGAACATATAATCGAAC
Found at i:43841 original size:21 final size:20
Alignment explanation
Indices: 43811--43851 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
43801 TACAAAGACT
* *
43811 TATAACATATTTTAACTTAAA
1 TATAAAATATCTTAA-TTAAA
43832 TATAAAATATCTTAATTAAA
1 TATAAAATATCTTAATTAAA
43852 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAAAATATCTTAATTAAA
Found at i:45113 original size:19 final size:18
Alignment explanation
Indices: 45085--45147 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
45075 TTTAGTGAAA
45085 TTTT-TTTTATTTGTAAT
1 TTTTATTTTATTTGTAAT
*
45102 TCTTTATTTTATTTTTAAAT
1 T-TTTATTTTATTTGT-AAT
*
45122 AATTTT-TTTTATTTGTTAT
1 --TTTTATTTTATTTGTAAT
45141 TTTTATT
1 TTTTATT
45148 CGTGCACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
17 5 0.14
18 5 0.14
19 11 0.30
20 12 0.32
21 3 0.08
22 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTATTTTATTTGTAAT
Found at i:45133 original size:20 final size:19
Alignment explanation
Indices: 45083--45137 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
45073 GTTTTAGTGA
45083 AATTTTTTTTATTTGTAAT
1 AATTTTTTTTATTTGTAAT
** * *
45102 TCTTTATTTTATTTTTAAAT
1 AATTTTTTTTATTTGT-AAT
45122 AATTTTTTTTATTTGT
1 AATTTTTTTTATTTGT
45138 TATTTTTATT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
AATTTTTTTTATTTGTAAT
Found at i:58395 original size:24 final size:25
Alignment explanation
Indices: 58363--58410 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
58353 AAATTCTTTG
58363 TATTATATAAATTTATTA-TTATAC
1 TATTATATAAATTTATTACTTATAC
* *
58387 TATTTTATAATTTTATTACTTATA
1 TATTATATAAATTTATTACTTATA
58411 TAAATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATATAAATTTATTACTTATAC
Found at i:68014 original size:31 final size:31
Alignment explanation
Indices: 67969--68028 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
67959 AAATTTTAAA
**
67969 ATTTAAAAAGTATAAGGACTAAAATTGACAT
1 ATTTAAAAAGTATAAAAACTAAAATTGACAT
*
68000 ATTTGAAAAA-TATAAAAATTAAAATTGAC
1 ATTT-AAAAAGTATAAAAACTAAAATTGAC
68029 CAAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (31 bp):
ATTTAAAAAGTATAAAAACTAAAATTGACAT
Found at i:68280 original size:5 final size:6
Alignment explanation
Indices: 68263--68288 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
68253 TAAAATTTAA
68263 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
68289 ATATTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:72614 original size:7 final size:8
Alignment explanation
Indices: 72597--72625 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
72587 TGTGTTTGTG
72597 TTTTTCTT
1 TTTTTCTT
72605 TTTTTCTT
1 TTTTTCTT
72613 TTTTTCTT
1 TTTTTCTT
72621 TTTTT
1 TTTTT
72626 TAATAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:73165 original size:18 final size:18
Alignment explanation
Indices: 73124--73200 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 18
73114 GCATTACTTT
* **
73124 TTAAAAATATTTTTGAGG
1 TTAAAAATATTTTTAAAA
*
73142 TCAAAAATATTTTTAAAA
1 TTAAAAATATTTTTAAAA
* *
73160 TTAAAAATAATTCT-AAA
1 TTAAAAATATTTTTAAAA
* *
73177 -TAAATA-ACTTTTAAAA
1 TTAAAAATATTTTTAAAA
73193 TTAAAAAT
1 TTAAAAAT
73201 GCTTTTGAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
15 4 0.09
16 8 0.18
17 8 0.18
18 25 0.56
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (18 bp):
TTAAAAATATTTTTAAAA
Found at i:73681 original size:8 final size:8
Alignment explanation
Indices: 73668--73695 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
73658 CGGTGGGATG
73668 CTCACTTT
1 CTCACTTT
73676 CTCACTTT
1 CTCACTTT
73684 CTCACTTT
1 CTCACTTT
73692 CTCA
1 CTCA
73696 ATGGGTCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.39, G:0.00, T:0.46
Consensus pattern (8 bp):
CTCACTTT
Found at i:76635 original size:26 final size:27
Alignment explanation
Indices: 76585--76639 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
76575 TTCTTCTCTT
*
76585 AAATCATTCATATATCCTTTCAAAATA
1 AAATCATTCATATATCATTTCAAAATA
76612 AAATCATTCATATAGT-ATTT-AAAATA
1 AAATCATTCATATA-TCATTTCAAAATA
76638 AA
1 AA
76640 CTTAATTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.31
27 17 0.65
28 1 0.04
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (27 bp):
AAATCATTCATATATCATTTCAAAATA
Found at i:78816 original size:21 final size:21
Alignment explanation
Indices: 78777--78818 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
78767 CTAATATAAT
* **
78777 TAAAATAATTAAATTATCAAA
1 TAAAATAATAAAAGGATCAAA
78798 TAAAATAATAAAAGGATCAAA
1 TAAAATAATAAAAGGATCAAA
78819 ATTAAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAAATAATAAAAGGATCAAA
Found at i:96034 original size:117 final size:117
Alignment explanation
Indices: 95901--96729 Score: 1157
Period size: 117 Copynumber: 7.0 Consensus size: 117
95891 TAGGCTTGGC
* * *
95901 CTTAAGGGGATCTTCCATTTCAACCCTGATATTACTTAACCCTTCAATGCTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
95966 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* *
96018 CTTAAGGGGATCTTCCATTTCAGCCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * * *
96083 CAATTTTCTTCTTCTTC--G----TTGAACCCTTTGGCCAACCATGTTTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* * * * **
96129 CTTAAGGGGATTTTCCATTTCAACCCAGCTGTCACTTAACCCTACAATACAATGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * *
96194 TAGTTTTCTTCTTCTTGTTGTTCATTTTACCCTTTGGCTGACCACATTTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
*
96246 CTTAAGGGGATCTTCCATTTCAACCTTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * * * *
96311 TAGTTTTCTTGTTATTGTTGTTTTTCTTTGAACCTTTTGGCCGACCACGTTTAGG
66 TAGTTTTCTTCTTCTTCTTG---TTCATTGTACCCTTTGGCCGACCACGTTTAGG
*
96366 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATACTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
96431 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
66 TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
*
96483 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACACTTCAATACTCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
96548 TAGTTTTCTTCTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
66 TAG-----TT-TTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
* * *
96606 CTTAAGGGGATCTTCCATTTCAACCTTGTTATCACTTAACCCTTCAATAATCTGTTCACCACCAA
1 CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
* * * * * * *
96671 TAGTTTTCTTCTTGTTGTTGTTTTTCTTTGAACCCTTTGGCCTACCACGCTTACG
66 TAGTTTTCTTCTTCTTCTTG---TTCATTGTACCCTTTGGCCGACCACGTTTAGG
96726 CTTA
1 CTTA
96730 GCCTGCTTAC
Statistics
Matches: 633, Mismatches: 61, Indels: 33
0.87 0.08 0.05
Matches are distributed among these distances:
111 96 0.15
113 1 0.00
115 1 0.00
117 283 0.45
118 2 0.00
120 137 0.22
122 2 0.00
123 111 0.18
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.39
Consensus pattern (117 bp):
CTTAAGGGGATCTTCCATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAA
TAGTTTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGG
Found at i:96454 original size:237 final size:235
Alignment explanation
Indices: 95851--96729 Score: 1180
Period size: 237 Copynumber: 3.7 Consensus size: 235
95841 ACTAGCAAGC
* *
95851 TTTTTCTGTTTATTCTTTGAACCTTTTGGCCGACCACGTTTAGGCTTGGCCTTAAGGGGATCTTC
1 TTTTTTTGTTTATTCTTTGAACCCTTTGGCCGACCACGTTTA-----GG-CTTAAGGGGATCTTC
* * *
95916 CATTTCAACCCTGATATTACTTAACCCTTCAATGCTCTGTTCACCACCAATAGTTTTCTTCTTCT
60 CATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCT
*
95981 TCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAGCCTTG
125 TCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTG
* *
96046 CTATCACTTAACCCTTCAATACTCTGTTCACCACCAACAATTTTC-
190 CTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCT
* * * * * *
96091 -----TT-CTTCTTCGTTGAACCCTTTGGCCAACCATGTTTAGGCTTAAGGGGATTTTCCATTTC
1 TTTTTTTGTTTATTCTTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTC
* * * ** *
96150 AACCCAGCTGTCACTTAACCCTACAATACAATGTTCACCACCAATAGTTTTCTTCTTCTTGTTGT
66 AACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGT
* * *
96215 TCATTTTACCCTTTGGCTGACCACATTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCA
131 TCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCA
96280 CTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCT
196 CTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCT
*
96320 TGTTATTGTTGTTT-TTCTTTGAACCTTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCAT
1 T-TT-TT-TTGTTTATTCTTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCAT
*
96384 TTCAACCCTGCTATCACTTAACACTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCT
63 TTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCT
*
96449 TGTTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCCTGCTA
128 TGTTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTA
*
96514 TCACTTAACACTTCAATACTCTGTTCACCACCAATAGTTTTCT
193 TCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCT
* * * *
96557 TCTTCTTCTTCTTCTTGTTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCC
1 T-TT-TT-TT-GT-TTATTCTTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCC
* * * *
96622 ATTTCAACCTTGTTATCACTTAACCCTTCAATAATCTGTTCACCACCAATAGTTTTCTTCTTGTT
61 ATTTCAACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTT
* * * * * *
96687 GTTGTTTTTCTTTGAACCCTTTGGCCTACCACGCTTACGCTTA
126 CTTG---TTCATTGTACCCTTTGGCCGACCACGTTTAGGCTTA
96730 GCCTGCTTAC
Statistics
Matches: 564, Mismatches: 59, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
228 174 0.31
229 2 0.00
234 28 0.05
235 1 0.00
237 215 0.38
238 3 0.01
239 2 0.00
240 108 0.19
243 31 0.05
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.39
Consensus pattern (235 bp):
TTTTTTTGTTTATTCTTTGAACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTC
AACCCTGCTATCACTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCTTCTTCTTCTTGT
TCATTGTACCCTTTGGCCGACCACGTTTAGGCTTAAGGGGATCTTCCATTTCAACCTTGCTATCA
CTTAACCCTTCAATACTCTGTTCACCACCAATAGTTTTCT
Found at i:114242 original size:16 final size:16
Alignment explanation
Indices: 114215--114250 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
114205 AGATAGAATT
114215 AAATAGAAATTAAATCA
1 AAATAGAAATTAAAT-A
114232 AAATA-AAATTAAATA
1 AAATAGAAATTAAATA
114247 AAAT
1 AAAT
114251 TTATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (16 bp):
AAATAGAAATTAAATA
Found at i:114990 original size:3 final size:3
Alignment explanation
Indices: 114982--115029 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
114972 ATAAATAAGC
114982 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
115030 CAAAATTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:115547 original size:20 final size:20
Alignment explanation
Indices: 115509--115548 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
115499 CAACCCTAAC
* *
115509 CATAGTGTTCTTTTTTAATT
1 CATAGTGTTCTCTTATAATT
*
115529 CATAGTGTTGTCTTATAATT
1 CATAGTGTTCTCTTATAATT
115549 ATATTGATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (20 bp):
CATAGTGTTCTCTTATAATT
Found at i:128583 original size:21 final size:21
Alignment explanation
Indices: 128541--128583 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
128531 AAAATACTGC
* *
128541 TGCTGTTTTTTACACTTTTTT
1 TGCTGTTTTTTAAACTTATTT
128562 TGCTGTTTTTTTAAAC-TATTT
1 TGCTG-TTTTTTAAACTTATTT
128583 T
1 T
128584 TCATTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.14, C:0.12, G:0.09, T:0.65
Consensus pattern (21 bp):
TGCTGTTTTTTAAACTTATTT
Found at i:129042 original size:329 final size:328
Alignment explanation
Indices: 128409--129056 Score: 1190
Period size: 329 Copynumber: 2.0 Consensus size: 328
128399 AGTTGAAGGG
* *
128409 TTTGTATAAAAATATAGGCTCAAAAATGAGTTTGAATCCTAAATGGACCAGTACTTTAAATGAGC
1 TTTGGATAAAAATATAAGCTCAAAAATGAGTTTGAATCCTAAATGGACCAGTACTTTAAATGAGC
*
128474 CAAACCTCGAGTAAGTTTTTTTGGCCTGAACCCGGCCTGACCCAAATTTGTAGAAAAAAAATACT
66 CAAACCTCGAGTAAGCTTTTTTGGCCTGAACCCGGCCTGACCCAAATTTGTAGAAAAAAAATACT
128539 GCTGCTGTTTTTTACACTTTTTTTGCTGTTTTTTTAAACTATTTTTCATTGTTTTGCTATCATTT
131 GCTGCTGTTTTTTACACTTTTTTTGCTGTTTTTTTAAACTATTTTTCATTGTTTTGCTATCATTT
128604 CGCTATTATATTGGTATTATTTTGTTATTATTTGGATATTGTATAACTATTGTTTTATTATTAAT
196 CGCTATTATATTGGTATTATTTTGTTATTATTTGGATATTGTATAACTATTGTTTTATTATTAAT
128669 TTTGCCACTATTTTACAGGTATTTGTTTGCTAAGTTGTGCTTATCTTAGTGTTATTTAAATTGGA
261 TTTGCCACTATTTTACAGGTATTTGTTTGCTAAGTTGTGCTTATCTTAGTGTTATTTAAATTGGA
128734 GGA
326 GGA
* * *
128737 TTTGGATAAAAATATAAGCTCAAAAATGTGTTTGAATTCTAAATGGACCGGTACTTTAAATGAGC
1 TTTGGATAAAAATATAAGCTCAAAAATGAGTTTGAATCCTAAATGGACCAGTACTTTAAATGAGC
* **
128802 CAAACCTTGAGTAAGCTTTTTTGGCCTGAATTCGGCCTGACCCAAATTTGTAGAAAAAAAATACT
66 CAAACCTCGAGTAAGCTTTTTTGGCCTGAACCCGGCCTGACCCAAATTTGTAGAAAAAAAATACT
128867 GCTGCTGTTTTTTACACTTTTTTTGCTGTTTTTTTTAAAC-AGTTTTTCATTGTTTTGCTATCAT
131 GCTGCTGTTTTTTACACTTTTTTTGCTG-TTTTTTTAAACTA-TTTTTCATTGTTTTGCTATCAT
128931 TTCGCTATTATATTGGTATTATTTTGTTATTATTTGGATATTGTATAACTATTGTTTTATTATTA
194 TTCGCTATTATATTGGTATTATTTTGTTATTATTTGGATATTGTATAACTATTGTTTTATTATTA
128996 ATTTTGCCACTATTTTACAGGTATTTGTTTGCTAAGTTGTGCTTATCTTAGTGTTATTTAA
259 ATTTTGCCACTATTTTACAGGTATTTGTTTGCTAAGTTGTGCTTATCTTAGTGTTATTTAA
129057 GTTTTTATTT
Statistics
Matches: 309, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
328 150 0.49
329 159 0.51
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (328 bp):
TTTGGATAAAAATATAAGCTCAAAAATGAGTTTGAATCCTAAATGGACCAGTACTTTAAATGAGC
CAAACCTCGAGTAAGCTTTTTTGGCCTGAACCCGGCCTGACCCAAATTTGTAGAAAAAAAATACT
GCTGCTGTTTTTTACACTTTTTTTGCTGTTTTTTTAAACTATTTTTCATTGTTTTGCTATCATTT
CGCTATTATATTGGTATTATTTTGTTATTATTTGGATATTGTATAACTATTGTTTTATTATTAAT
TTTGCCACTATTTTACAGGTATTTGTTTGCTAAGTTGTGCTTATCTTAGTGTTATTTAAATTGGA
GGA
Found at i:131821 original size:30 final size:30
Alignment explanation
Indices: 131746--131821 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
131736 AATTGATTTG
* *
131746 ATTAATTTATATTTATTCTTTTAATGAGATT
1 ATTAA-TTATATTTATTCTTTTAAAGAAATT
* **
131777 ATTACTTACCTTTATT-TTTTGAAAGAAATT
1 ATTAATTATATTTATTCTTTT-AAAGAAATT
131807 ATTAATTATATTTAT
1 ATTAATTATATTTAT
131822 ATAAAGCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 4 0.11
30 28 0.78
31 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (30 bp):
ATTAATTATATTTATTCTTTTAAAGAAATT
Found at i:132367 original size:31 final size:31
Alignment explanation
Indices: 132313--132400 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
132303 TCATTGTGCT
132313 CTTCAAAA-TTTT-GAATATTTTAATTA-AGTC
1 CTTCAAAACTTTTAGAA-ATTTTAATTATA-TC
132343 CTTCAAAACTTTTAGAAATTTTAATTATATC
1 CTTCAAAACTTTTAGAAATTTTAATTATATC
* * *
132374 TTTCAAAACTTTCAAAAATTTTAATTA
1 CTTCAAAACTTTTAGAAATTTTAATTA
132401 GATCATCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
30 8 0.15
31 40 0.77
32 4 0.08
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (31 bp):
CTTCAAAACTTTTAGAAATTTTAATTATATC
Found at i:138171 original size:8 final size:8
Alignment explanation
Indices: 138158--138207 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
138148 TTTTATATTG
138158 TTTTAATA
1 TTTTAATA
138166 TTTTAATA
1 TTTTAATA
*
138174 ATTTAAT-
1 TTTTAATA
138181 TTTTAA-A
1 TTTTAATA
138188 CTTATTAATA
1 -TT-TTAATA
*
138198 TATTAATA
1 TTTTAATA
138206 TT
1 TT
138208 GATCACACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 5 0.15
8 23 0.68
9 5 0.15
10 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTTAATA
Found at i:146515 original size:3 final size:3
Alignment explanation
Indices: 146509--146533 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
146499 CCTGCAAAAA
146509 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
146534 TGATGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:147870 original size:13 final size:13
Alignment explanation
Indices: 147852--147878 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
147842 ATCCTTACCA
147852 AACTATAGCAACT
1 AACTATAGCAACT
147865 AACTATAGCAACT
1 AACTATAGCAACT
147878 A
1 A
147879 GATATTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
AACTATAGCAACT
Found at i:163820 original size:82 final size:82
Alignment explanation
Indices: 163683--163849 Score: 325
Period size: 82 Copynumber: 2.0 Consensus size: 82
163673 ATAATTTAAC
163683 AGAAAATAATTTTTTTAAAGTCATTATGGCTAATTGCTTTTGCCTAATTCTTCAATTTTCAACCT
1 AGAAAATAATTTTTTTAAAGTCATTATGGCTAATTGCTTTTGCCTAATTCTTCAATTTTCAACCT
163748 CTTAAAAGAATTCAAGT
66 CTTAAAAGAATTCAAGT
*
163765 AGAAAATAATTTTTTTAAAGTGATTATGGCTAATTGCTTTTGCCTAATTCTTCAATTTTCAACCT
1 AGAAAATAATTTTTTTAAAGTCATTATGGCTAATTGCTTTTGCCTAATTCTTCAATTTTCAACCT
163830 CTTAAAAGAATTCAAGT
66 CTTAAAAGAATTCAAGT
163847 AGA
1 AGA
163850 GTGAGAGGAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (82 bp):
AGAAAATAATTTTTTTAAAGTCATTATGGCTAATTGCTTTTGCCTAATTCTTCAATTTTCAACCT
CTTAAAAGAATTCAAGT
Found at i:165874 original size:18 final size:17
Alignment explanation
Indices: 165841--165877 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
165831 ATAGAATGAG
*
165841 AATAAATTTTTTAATTA
1 AATAAATTTATTAATTA
165858 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
165876 AA
1 AA
165878 ATTTTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:171735 original size:6 final size:6
Alignment explanation
Indices: 171724--171754 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
171714 ACAGTCTCTG
171724 GTCCTT GTCCTT GTCCTT GTCCTT GGTCCTT
1 GTCCTT GTCCTT GTCCTT GTCCTT -GTCCTT
171755 TATTGCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.00, C:0.32, G:0.19, T:0.48
Consensus pattern (6 bp):
GTCCTT
Found at i:171741 original size:12 final size:13
Alignment explanation
Indices: 171722--171754 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
171712 GAACAGTCTC
171722 TGGTCCTTGTCCT
1 TGGTCCTTGTCCT
171735 T-GTCCTTGTCCT
1 TGGTCCTTGTCCT
171747 TGGTCCTT
1 TGGTCCTT
171755 TATTGCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.00, C:0.30, G:0.21, T:0.48
Consensus pattern (13 bp):
TGGTCCTTGTCCT
Found at i:172670 original size:17 final size:17
Alignment explanation
Indices: 172648--172681 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
172638 TTTTTTCCCC
172648 ATATAATAATCATAATT
1 ATATAATAATCATAATT
172665 ATATAATAATCATAATT
1 ATATAATAATCATAATT
172682 GGCCGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATAATCATAATT
Found at i:175595 original size:11 final size:11
Alignment explanation
Indices: 175579--175603 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
175569 CTCATGCTCG
175579 AAATAAATAAA
1 AAATAAATAAA
175590 AAATAAATAAA
1 AAATAAATAAA
175601 AAA
1 AAA
175604 AATCCAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:176484 original size:10 final size:10
Alignment explanation
Indices: 176471--176499 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
176461 AAAAAAAAAA
176471 AAAAAAGCTT
1 AAAAAAGCTT
176481 AAAAAAGCTT
1 AAAAAAGCTT
176491 AAAAAAGCT
1 AAAAAAGCT
176500 CAATTCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAAAAGCTT
Found at i:181437 original size:2 final size:2
Alignment explanation
Indices: 181430--181455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
181420 GTGAATAAAC
181430 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
181456 TACTATGGAC
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:182121 original size:25 final size:25
Alignment explanation
Indices: 182074--182121 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
182064 AACATATTGC
* *
182074 ATATACAAATAATTATATTTATTCA
1 ATATAAAAATAATTATATGTATTCA
182099 ATATAAAAATAATT-TAATGTATT
1 ATATAAAAATAATTAT-ATGTATT
182122 TAGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
ATATAAAAATAATTATATGTATTCA
Found at i:197880 original size:22 final size:23
Alignment explanation
Indices: 197833--197882 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
197823 AACAAGAAAC
* *
197833 ACAAAACACAAAGAACAAGTTTA
1 ACAAAACACAAAGAACAAATTAA
197856 ACAAAA-ACAAAG-ACTAAATTAA
1 ACAAAACACAAAGAAC-AAATTAA
197878 ACAAA
1 ACAAA
197883 CAAAACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12
Consensus pattern (23 bp):
ACAAAACACAAAGAACAAATTAA
Found at i:198614 original size:15 final size:14
Alignment explanation
Indices: 198575--198618 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
198565 TATAAATCTT
*
198575 AGAATTTATTTTTT
1 AGAATTTATTTTTG
*
198589 ACAATTTATTTTTG
1 AGAATTTATTTTTG
198603 AGAATTTAATTTTTG
1 AGAATTT-ATTTTTG
198618 A
1 A
198619 TCTTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (14 bp):
AGAATTTATTTTTG
Found at i:205501 original size:20 final size:21
Alignment explanation
Indices: 205464--205502 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
205454 AATAGGTTAT
205464 TTAAGTTAAAAAAATTATTAA
1 TTAAGTTAAAAAAATTATTAA
* *
205485 TTAA-TTAAATAAGTTATT
1 TTAAGTTAAAAAAATTATT
205503 TTTAAAGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAAGTTAAAAAAATTATTAA
Found at i:209987 original size:66 final size:66
Alignment explanation
Indices: 209906--210036 Score: 262
Period size: 66 Copynumber: 2.0 Consensus size: 66
209896 AACATATACA
209906 TTCATTTTAAAACCTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGGAGTTATTTTTTAA
1 TTCATTTTAAAACCTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGGAGTTATTTTTTAA
209971 T
66 T
209972 TTCATTTTAAAACCTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGGAGTTATTTTTTAA
1 TTCATTTTAAAACCTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGGAGTTATTTTTTAA
210037 ATTGCATGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (66 bp):
TTCATTTTAAAACCTTTTTTTAGATAATTACGTTTATTTTCATTAAATTAGGAGTTATTTTTTAA
T
Found at i:211975 original size:31 final size:31
Alignment explanation
Indices: 211940--212002 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
211930 TACAAAATGA
*
211940 TCACTAAACTTTTCAAAAAATTTCATTTAAG
1 TCACTAAACTATTCAAAAAATTTCATTTAAG
** *
211971 TCACTAAACTATTCAAAAGTTTTTATTTAAG
1 TCACTAAACTATTCAAAAAATTTCATTTAAG
212002 T
1 T
212003 GATCAGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAAATTTCATTTAAG
Found at i:212170 original size:7 final size:7
Alignment explanation
Indices: 212154--212183 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
212144 TGTAGGAGAT
212154 AAAAAA-
1 AAAAAAG
212160 AAAAAAG
1 AAAAAAG
212167 AAAAAAG
1 AAAAAAG
212174 AAAAAAG
1 AAAAAAG
212181 AAA
1 AAA
212184 GATGTTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:218624 original size:21 final size:20
Alignment explanation
Indices: 218582--218626 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
218572 CATAATTTGA
*
218582 TTTTTTTAAATAAAAAATAT
1 TTTTTTTAAATAAAAAACAT
* *
218602 TTTTTTTAAAATTATAAACAT
1 TTTTTTT-AAATAAAAAACAT
218623 TTTT
1 TTTT
218627 AAAATCATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTTTAAATAAAAAACAT
Found at i:221477 original size:12 final size:12
Alignment explanation
Indices: 221459--221489 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
221449 GTACTAGAGA
221459 AGGTGGTGGTGG
1 AGGTGGTGGTGG
*
221471 CGGTGGTGGTGG
1 AGGTGGTGGTGG
221483 AGGTGGT
1 AGGTGGT
221490 TGTGCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.65, T:0.26
Consensus pattern (12 bp):
AGGTGGTGGTGG
Found at i:222127 original size:19 final size:19
Alignment explanation
Indices: 222103--222141 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
222093 GTGGATATTA
222103 AAATTTATTATTATACTTT
1 AAATTTATTATTATACTTT
* * *
222122 AAATTTGTTGTTATATTTT
1 AAATTTATTATTATACTTT
222141 A
1 A
222142 TAAATAATGT
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:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
AAATTTATTATTATACTTT
Found at i:224868 original size:6 final size:6
Alignment explanation
Indices: 224846--224893 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
224836 TATTTATAAA
* *
224846 TTTTAT ATTTAGT TTTTAA TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
224894 AGAATTTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:225131 original size:14 final size:15
Alignment explanation
Indices: 225112--225149 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
225102 AAAATAAAGT
225112 AATTAAATTCTT-AA
1 AATTAAATTCTTAAA
*
225126 AATTAAATTTTTAAA
1 AATTAAATTCTTAAA
225141 AATTAAATT
1 AATTAAATT
225150 AAGAGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATTCTTAAA
Found at i:227498 original size:16 final size:17
Alignment explanation
Indices: 227472--227518 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
227462 ATTTTTTATA
227472 TATT-TAGTTTTTATTT
1 TATTATAGTTTTTATTT
*
227488 TTTTATA-TTTTTATTT
1 TATTATAGTTTTTATTT
227504 TATTATAGTTTTTAT
1 TATTATAGTTTTTAT
227519 CTATCTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (17 bp):
TATTATAGTTTTTATTT
Found at i:227504 original size:21 final size:22
Alignment explanation
Indices: 227463--227507 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
227453 TTTCCCTTAA
227463 TTTTTTATATATTTAGTTTTTAT
1 TTTTTTATATATTTAG-TTTTAT
*
227486 TTTTTTATATTTTTA-TTTTAT
1 TTTTTTATATATTTAGTTTTAT
227507 T
1 T
227508 ATAGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
23 14 0.67
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTTATATATTTAGTTTTAT
Found at i:229319 original size:29 final size:29
Alignment explanation
Indices: 229287--229536 Score: 151
Period size: 29 Copynumber: 8.6 Consensus size: 29
229277 AATTCGAGGT
*
229287 TAAAAATGGAATTTTTAGACA-TTCGGGGG
1 TAAAAATGGAATTTTTGGA-AGTTCGGGGG
* * *
229316 T-AAAAGGGTATTTTT-GAGAGTTTC-GAGG
1 TAAAAATGGAATTTTTGGA-AG-TTCGGGGG
* * * *
229344 TCGAAAATGGAGTTTTTTGATA-TTCGAGGG
1 T-AAAAATGGAATTTTTGGA-AGTTCGGGGG
* **
229374 T-AAACTGGTAATTTTTGGAAGTTTAGGGG
1 TAAAAATGG-AATTTTTGGAAGTTCGGGGG
229403 TAAAAATGGAATTTTTGGAAGTTC-GGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGGGG
* * *
229431 TCAAAAAT-GAGATTTTTGAAAGTTTAGGGGT
1 T-AAAAATGGA-ATTTTTGGAAG-TTCGGGGG
* *
229462 TAACAATGGAATTTTTGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGGGG
* *
229491 T-AAAATGGAAATTTTT-GAAGTTTCGAGGT
1 TAAAAATGG-AATTTTTGGAAG-TTCGGGGG
*
229520 TAAAAAATGAAATTTTT
1 T-AAAAATGGAATTTTT
229537 AGGAGTTTTA
Statistics
Matches: 174, Mismatches: 29, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.02
28 40 0.23
29 72 0.41
30 44 0.25
31 15 0.09
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGGGGG
Found at i:229369 original size:87 final size:86
Alignment explanation
Indices: 229276--229536 Score: 244
Period size: 88 Copynumber: 3.0 Consensus size: 86
229266 AAGTTTGGGA
* *
229276 AAATTCGAGGTTAAAAATGGAATTTTTAGACA-TTCGGGGGTAAAAGGGTATTTTTGAGAGTTTC
1 AAATTCGAGGTTAAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAGGGAATTTTTGAGAGTTTC
* *
229340 GAGGTCGAAAATGGAGTTTTTTG
65 GAGGTCAAAAAT-GAGATTTTTG
* * * ** *
229363 ATATTCGAGGGT-AAACTGGTAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTG-GAAG-T
1 AAATTCGAGGTTAAAAATGG-AATTTTTGGAAGTTCGGGGGT-AAAAGGGAATTTTTGAG-AGTT
*
229425 TCGGGGTCAAAAATGAGATTTTTG
63 TCGAGGTCAAAAATGAGATTTTTG
* * * * *
229449 AAAGTTTAGGGGTTAACAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAAATTTTTGA-AGTT
1 AAA--TTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAA-GGGAATTTTTGAGAGTT
* *
229513 TCGAGGTTAAAAAATGAAATTTTT
63 TCGAGG-TCAAAAATGAGATTTTT
229537 AGGAGTTTTA
Statistics
Matches: 138, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
86 18 0.13
87 46 0.33
88 54 0.39
89 20 0.14
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (86 bp):
AAATTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAGGGAATTTTTGAGAGTTTCG
AGGTCAAAAATGAGATTTTTG
Found at i:229484 original size:59 final size:58
Alignment explanation
Indices: 229284--229580 Score: 239
Period size: 58 Copynumber: 5.1 Consensus size: 58
229274 GAAAATTCGA
* * ** * *
229284 GGTTAAAAATGGAATTTTTAGACA-TTCGGGGGTAAAA-GGGTATTTTTGAGAGTTTCGA
1 GGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAATGGAAATTTTTGA-AGTTTAGG
** * * * *
229342 GGTCGAAAATGGAGTTTTTTGATA-TTCGAGGGTAAACTGGTAATTTTTGGAAGTTTAGG
1 GGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAATGGAAATTTTT-GAAGTTTAGG
*
229401 GG-TAAAAATGGAATTTTTGGAAGTTCG-GGGTCAAAAAT-GAGATTTTTGAAAGTTTAGG
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGT--AAAATGGAAATTTTTG-AAGTTTAGG
* * *
229459 GGTTAACAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAAATTTTTGAAGTTTCGA
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAAATTTTTGAAGTTTAGG
* ** * ** *
229517 GGTTAAAAAATGAAATTTTTAGG-AGTTTTAGGGTCAAATATATAATTTTTGGAAGTTTCGG
1 GGTT-AAAAATGGAATTTTT-GGAAGTTCGAGGGTAAAATGGA-AATTTTT-GAAGTTTAGG
229578 GGT
1 GGT
229581 CCTTCAGAGC
Statistics
Matches: 196, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
57 6 0.03
58 83 0.42
59 80 0.41
60 15 0.08
61 12 0.06
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (58 bp):
GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAAATTTTTGAAGTTTAGG
Found at i:229581 original size:30 final size:29
Alignment explanation
Indices: 229382--229581 Score: 135
Period size: 30 Copynumber: 6.8 Consensus size: 29
229372 GGTAAACTGG
* * *
229382 TAATTTTTGGAAGTTTAGGGGTAAAAATG
1 TAATTTTTGGAAGTTTCGGGGTCAAAATA
*
229411 GAATTTTTGGAAG-TTCGGGGTCAAAA-A
1 TAATTTTTGGAAGTTTCGGGGTCAAAATA
* * * *
229438 TGAGATTTTTGAAAGTTTAGGGGTTAACAATG
1 T-A-ATTTTTGGAAGTTTCGGGGTCAA-AATA
*
229470 GAATTTTTGGAAG-TTCGAGGGT-AAAATGGA
1 TAATTTTTGGAAGTTTCG-GGGTCAAAAT--A
* * *
229500 -AATTTTT-GAAGTTTCGAGGTTAAAAAA
1 TAATTTTTGGAAGTTTCGGGGTCAAAATA
**
229527 TGAAATTTTTAGG-AGTTTTAGGGTCAAATATA
1 T--AATTTTT-GGAAGTTTCGGGGTCAAA-ATA
229559 TAATTTTTGGAAGTTTCGGGGTC
1 TAATTTTTGGAAGTTTCGGGGTC
229582 CTTCAGAGCA
Statistics
Matches: 132, Mismatches: 22, Indels: 33
0.71 0.12 0.18
Matches are distributed among these distances:
27 1 0.01
28 22 0.17
29 44 0.33
30 47 0.36
31 14 0.11
32 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTCGGGGTCAAAATA
Found at i:231174 original size:17 final size:17
Alignment explanation
Indices: 231164--231243 Score: 92
Period size: 17 Copynumber: 4.6 Consensus size: 17
231154 TAAATAGATT
231164 TAAATTTTAAA-TTTATAA
1 TAAA-TTTAAATTTTA-AA
231182 TAAATTTAAATTTTAAA
1 TAAATTTAAATTTTAAA
* * *
231199 TAAATTTTAACTTAAAA
1 TAAATTTAAATTTTAAA
231216 TAAATTT-AATTTTAAAA
1 TAAATTTAAATTTT-AAA
231233 TAAATTTAAAT
1 TAAATTTAAAT
231244 CTTGTTGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
16 4 0.07
17 39 0.72
18 11 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTTAAA
Found at i:231188 original size:24 final size:23
Alignment explanation
Indices: 231151--231199 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
231141 ATTGGACTTG
*
231151 ATTTAAATAGATTTAAATTTTAA
1 ATTTAAATAAATTTAAATTTTAA
231174 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAATTTTAA
231198 AT
1 AT
231200 AAATTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTTAA
Found at i:231218 original size:34 final size:35
Alignment explanation
Indices: 231164--231239 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
231154 TAAATAGATT
* *
231164 TAAATTTTAAATTTATAATAAATTTAAATTTT-AAA
1 TAAATTTTAAACTTAAAATAAATTT-AATTTTAAAA
231199 TAAATTTT-AACTTAAAATAAATTTAATTTTAAAA
1 TAAATTTTAAACTTAAAATAAATTTAATTTTAAAA
231233 TAAATTT
1 TAAATTT
231240 AAATCTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 6 0.16
34 24 0.63
35 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (35 bp):
TAAATTTTAAACTTAAAATAAATTTAATTTTAAAA
Found at i:247264 original size:2 final size:2
Alignment explanation
Indices: 247259--247283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
247249 ATATATATAT
247259 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
247284 TGTTTGAACA
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:260471 original size:29 final size:31
Alignment explanation
Indices: 260420--260485 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
260410 TATAAAAATG
260420 ATAAATTTATTATTATATCAATTAAAATTAT
1 ATAAATTTATTATTATATCAATTAAAATTAT
*
260451 ATAAATTTATTATTA-CT-AATTAAAATTAT
1 ATAAATTTATTATTATATCAATTAAAATTAT
*
260480 GTAAAT
1 ATAAAT
260486 ATTAGGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 17 0.52
30 1 0.03
31 15 0.45
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (31 bp):
ATAAATTTATTATTATATCAATTAAAATTAT
Found at i:268265 original size:21 final size:21
Alignment explanation
Indices: 268241--268280 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
268231 TTGCTTTTTT
*
268241 TTTTATTTTTATTAAATTTGA
1 TTTTATTTTAATTAAATTTGA
268262 TTTTATTTTAATTAAATTT
1 TTTTATTTTAATTAAATTT
268281 TGTTTGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTATTTTAATTAAATTTGA
Found at i:276726 original size:45 final size:39
Alignment explanation
Indices: 276632--276711 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
276622 TCAAATTTGG
276632 AAAGAAAAAAGGATTCAAAATGGGTTAGAGTTAGAGGCT
1 AAAGAAAAAAGGATTCAAAATGGGTTAGAGTTAGAGGCT
276671 AAAGAAAAAAGGATTCAAAATGGGTTAGAGTTAGAGGCT
1 AAAGAAAAAAGGATTCAAAATGGGTTAGAGTTAGAGGCT
276710 AA
1 AA
276712 GTTCGCATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (39 bp):
AAAGAAAAAAGGATTCAAAATGGGTTAGAGTTAGAGGCT
Found at i:301822 original size:23 final size:23
Alignment explanation
Indices: 301788--301893 Score: 96
Period size: 23 Copynumber: 4.7 Consensus size: 23
301778 AGTGTTGGGA
*
301788 AAAT-AGTAAGCACACATAGTGC
1 AAATCAGTAAGCACACATAGCGC
*
301810 -AATCCAGTAAGCACACACAGCGC
1 AAAT-CAGTAAGCACACATAGCGC
* *
301833 -AATCAGTAGGCGCACATAGCGC
1 AAATCAGTAAGCACACATAGCGC
* *
301855 AAATCAGTAGGCACACA-AGGTGC
1 AAATCAGTAAGCACACATA-GCGC
301878 GAAA-CAGTAAGCACAC
1 -AAATCAGTAAGCACAC
301894 GAAGTGCGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
21 3 0.04
22 17 0.24
23 48 0.68
24 3 0.04
ACGTcount: A:0.41, C:0.25, G:0.22, T:0.12
Consensus pattern (23 bp):
AAATCAGTAAGCACACATAGCGC
Found at i:301900 original size:23 final size:23
Alignment explanation
Indices: 301859--301912 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
301849 TAGCGCAAAT
*
301859 CAGTAGGCACACAAGGTGCGAAA
1 CAGTAAGCACACAAGGTGCGAAA
301882 CAGTAAGCACACGAA-GTGCGAAA
1 CAGTAAGCACAC-AAGGTGCGAAA
301905 CAGTAAGC
1 CAGTAAGC
301913 GCACTTGCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.41, C:0.22, G:0.28, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACAAGGTGCGAAA
Found at i:302662 original size:28 final size:23
Alignment explanation
Indices: 302605--302651 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
302595 CTGTCCAATC
302605 TGTTTCAATGAAAACATTTTCTT
1 TGTTTCAATGAAAACATTTTCTT
302628 TGTTTCAATGAAAACATTTTCTT
1 TGTTTCAATGAAAACATTTTCTT
302651 T
1 T
302652 CTCATGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.49
Consensus pattern (23 bp):
TGTTTCAATGAAAACATTTTCTT
Found at i:311070 original size:12 final size:12
Alignment explanation
Indices: 311053--311086 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
311043 ACATTCAAAC
311053 AACAAAAATAGT
1 AACAAAAATAGT
*
311065 AACAAAAACAGT
1 AACAAAAATAGT
*
311077 AACACAAATA
1 AACAAAAATA
311087 ACAACAGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.12
Consensus pattern (12 bp):
AACAAAAATAGT
Found at i:311141 original size:25 final size:25
Alignment explanation
Indices: 311099--311156 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
311089 AACAGCAAAT
**
311099 TAAT-AAAAAAAAGTACCAAAACAA
1 TAATAAAAAAAAAACACCAAAACAA
311123 TAATAAAAAAAAAACACCAAAACAA
1 TAATAAAAAAAAAACACCAAAACAA
*
311148 CAA-AAAAAA
1 TAATAAAAAA
311157 GCAACCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.76, C:0.14, G:0.02, T:0.09
Consensus pattern (25 bp):
TAATAAAAAAAAAACACCAAAACAA
Found at i:311163 original size:22 final size:22
Alignment explanation
Indices: 311128--311181 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
311118 AACAATAATA
*
311128 AAAAAAAAAC-ACCAAAACAAC
1 AAAAAAAAGCAACCAAAACAAC
* **
311149 AAAAAAAAGCAACCAAAATAGT
1 AAAAAAAAGCAACCAAAACAAC
311171 AAAAAAAAGCA
1 AAAAAAAAGCA
311182 TCAAAAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.74, C:0.17, G:0.06, T:0.04
Consensus pattern (22 bp):
AAAAAAAAGCAACCAAAACAAC
Found at i:316592 original size:3 final size:3
Alignment explanation
Indices: 316584--316612 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
316574 GTACAACATT
316584 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
316613 TGTAAGATCA
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:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:316823 original size:2 final size:2
Alignment explanation
Indices: 316816--316846 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
316806 TAGTTACAAC
316816 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
316847 GAGAGAGAGA
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:316851 original size:2 final size:2
Alignment explanation
Indices: 316846--316887 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
316836 ATATATATAT
316846 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
316888 CATGGATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:322605 original size:2 final size:2
Alignment explanation
Indices: 322558--322588 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
322548 ATGCGATCAC
*
322558 AT AT TT 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
322589 GGAGGATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:338821 original size:12 final size:12
Alignment explanation
Indices: 338804--338829 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
338794 CACCACCTTT
338804 AAAAAAAAGAAA
1 AAAAAAAAGAAA
338816 AAAAAAAAGAAA
1 AAAAAAAAGAAA
338828 AA
1 AA
338830 GGTGAAGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:339282 original size:37 final size:37
Alignment explanation
Indices: 339228--339302 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
339218 GTTAGAAATA
*
339228 CACGTAGCCAAGTTTTTTTGGTCAACACGTTATTGTC
1 CACGTAGCCAAGGTTTTTTGGTCAACACGTTATTGTC
339265 CACGTAGCCAAGGTTTTTTGGTCAACACGTTATTGTC
1 CACGTAGCCAAGGTTTTTTGGTCAACACGTTATTGTC
339302 C
1 C
339303 TCACCAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (37 bp):
CACGTAGCCAAGGTTTTTTGGTCAACACGTTATTGTC
Found at i:339655 original size:21 final size:20
Alignment explanation
Indices: 339615--339657 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
339605 TTTATTCTCC
*
339615 TAATATAATCTTATTTTATT
1 TAATATAATCTTATTATATT
339635 TAATGATAATCATTA-TATATT
1 TAAT-ATAATC-TTATTATATT
339656 TA
1 TA
339658 TTTATGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATATAATCTTATTATATT
Found at i:340776 original size:3 final size:3
Alignment explanation
Indices: 340768--340793 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
340758 CAGGACGTCC
340768 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
340794 CTCACTGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:342396 original size:15 final size:15
Alignment explanation
Indices: 342373--342403 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
342363 TATAATTTTT
342373 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
*
342388 TATATAATTCTAAAA
1 TATAAAATTCTAAAA
342403 T
1 T
342404 TCTAAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAAAATTCTAAAA
Found at i:343408 original size:15 final size:15
Alignment explanation
Indices: 343388--343422 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
343378 AGAACATGAC
* *
343388 GACGACGATGAGGAT
1 GACGACGACGACGAT
343403 GACGACGACGACGAT
1 GACGACGACGACGAT
343418 GACGA
1 GACGA
343423 TGATAAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.37, T:0.09
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:343411 original size:21 final size:21
Alignment explanation
Indices: 343385--343425 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
343375 GAAAGAACAT
*
343385 GACGACGACGATGAGGATGAC
1 GACGACGACGATGACGATGAC
343406 GACGACGACGATGACGATGA
1 GACGACGACGATGACGATGA
343426 TAAGGAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.37, T:0.10
Consensus pattern (21 bp):
GACGACGACGATGACGATGAC
Found at i:353837 original size:24 final size:25
Alignment explanation
Indices: 353810--353874 Score: 60
Period size: 29 Copynumber: 2.4 Consensus size: 25
353800 TTTTGTCTCA
353810 CATTATAATAT-TTAATTTCATCGT
1 CATTATAATATATTAATTTCATCGT
*
353834 CATTACTATTTTTATATTAATTTCATCGT
1 CATTA-TA---ATATATTAATTTCATCGT
353863 CACCTTATAATA
1 CA--TTATAATA
353875 ATTGGAGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
27 2 0.06
28 3 0.09
29 15 0.47
30 2 0.06
31 3 0.09
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.49
Consensus pattern (25 bp):
CATTATAATATATTAATTTCATCGT
Found at i:354494 original size:217 final size:214
Alignment explanation
Indices: 354083--354494 Score: 462
Period size: 217 Copynumber: 1.9 Consensus size: 214
354073 AAAATAATGA
* *
354083 TACGTGAGAGTGTACGAGCTGTTTGCATGATTCTTTTATAGTGAGAGACAAATTTAGTTATATGT
1 TACGTGAGAGTGTACGAGCTGTTTGCATGATTCTTTTATAGTGAGAGACAAACTTAGTTACATGT
* *
354148 CTTGAGGTCACTAACATGAAAGTTTGATTCAATACTCTGTATATTGATAATGAGATTACATCCTA
66 CTTGAGCTCACTAACATGAAAGTTTGATTCAATACTCTGTATA-TGATAACGAGATTACATCCTA
* * ** * *
354213 AGATGATACGTCTTAAGACGATTCACAATCAATGACCATGTACTTTTTCGCAATCGCTATAAAAT
130 AGATGATACGTCTTAAGACAACTCACAATCAATGACCA-GTACTTCATCGCAATCCCCATAAAAT
354278 TTTAATTGAGAAAGGACATAG
194 TTTAATTGAGAAAGGACATAG
* * * * * *
354299 TACGTTAGAGTGTATGAGTTGTTTGCATGGTCTTTTTTATAGTGAGAGACAAGCTTAGTTACATG
1 TACGTGAGAGTGTACGAGCTGTTTGCATGAT-TCTTTTATAGTGAGAGACAAACTTAGTTACATG
*
354364 TCTTGAGACT-ACTAATATGGAAA-TTTGATTCAA-ATCTCCTG-ATA-G-TAACGATGATGCTA
65 TCTTGAG-CTCACTAACAT-GAAAGTTTGATTCAATA-CT-CTGTATATGATAACGA-GAT--TA
* * **
354423 CATCTTAAGATGATACGTCTTAAGACAACTGACAATCAATGATCCCA-TACTTCCAT-GTGATCC
123 CATCCTAAGATGATACGTCTTAAGACAACTCACAATCAATGA--CCAGTACTT-CATCGCAATCC
354486 CCATAAAAT
185 CCATAAAAT
354495 CTAAGTTAAA
Statistics
Matches: 164, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
214 5 0.03
215 4 0.02
216 28 0.17
217 115 0.70
218 9 0.05
219 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (214 bp):
TACGTGAGAGTGTACGAGCTGTTTGCATGATTCTTTTATAGTGAGAGACAAACTTAGTTACATGT
CTTGAGCTCACTAACATGAAAGTTTGATTCAATACTCTGTATATGATAACGAGATTACATCCTAA
GATGATACGTCTTAAGACAACTCACAATCAATGACCAGTACTTCATCGCAATCCCCATAAAATTT
TAATTGAGAAAGGACATAG
Found at i:372096 original size:16 final size:17
Alignment explanation
Indices: 372065--372099 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
372055 TTGATTCTGG
*
372065 ATTTTTAGTAATTTTTA
1 ATTTTTAGTAAATTTTA
372082 ATTTTTA-TAAATTTTA
1 ATTTTTAGTAAATTTTA
372098 AT
1 AT
372100 GATTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTTAGTAAATTTTA
Found at i:396827 original size:13 final size:13
Alignment explanation
Indices: 396809--396833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
396799 TATAACGTAA
396809 CAAAATTTTTAAT
1 CAAAATTTTTAAT
396822 CAAAATTTTTAA
1 CAAAATTTTTAA
396834 CCAATGATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
CAAAATTTTTAAT
Found at i:397119 original size:3 final size:3
Alignment explanation
Indices: 397111--397136 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
397101 ACCTTATGCT
397111 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
397137 TATAGCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:400844 original size:31 final size:32
Alignment explanation
Indices: 400803--400871 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
400793 AAATGTTGGG
* *
400803 AAAAAAAATTTTGAGTC-CCTTAAAAATTGATC
1 AAAAAAATTTTTG-GGCACCTTAAAAATTGATC
* *
400835 AAAAGAATTTTTGGGCACCTTAAAAATTGGT-
1 AAAAAAATTTTTGGGCACCTTAAAAATTGATC
400866 AAAAAA
1 AAAAAA
400872 TTTGGGCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (32 bp):
AAAAAAATTTTTGGGCACCTTAAAAATTGATC
Found at i:403098 original size:21 final size:20
Alignment explanation
Indices: 403055--403096 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
403045 TCAAATAAAC
*
403055 TTAAAAATATTAAAACAAAT
1 TTAAAAAAATTAAAACAAAT
403075 TTAAAATAAATTAAAA-AAAT
1 TTAAAA-AAATTAAAACAAAT
403095 TT
1 TT
403097 TATATTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAAATTAAAACAAAT
Found at i:403539 original size:12 final size:12
Alignment explanation
Indices: 403454--403558 Score: 76
Period size: 12 Copynumber: 9.1 Consensus size: 12
403444 AAAAACGCAT
*
403454 AAAAATAACATC
1 AAAAATAACAGC
403466 -AAAATAAC--C
1 AAAAATAACAGC
* *
403475 -AAAATAATAAC
1 AAAAATAACAGC
* *
403486 TAAAACAACAGC
1 AAAAATAACAGC
* *
403498 -AAAACAACAAC
1 AAAAATAACAGC
*
403509 AAAAAAAAGCAGC
1 AAAAATAA-CAGC
*
403522 AAAAATAGCAGC
1 AAAAATAACAGC
*
403534 AAAAATAACAAC
1 AAAAATAACAGC
403546 AAAAATAACAGC
1 AAAAATAACAGC
403558 A
1 A
403559 TCAAAACAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
9 8 0.11
11 19 0.25
12 40 0.53
13 9 0.12
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAATAACAGC
Found at i:403598 original size:12 final size:12
Alignment explanation
Indices: 403583--403659 Score: 68
Period size: 12 Copynumber: 6.5 Consensus size: 12
403573 AAATAGCACA
403583 AAAACAGCAACC
1 AAAACAGCAACC
* * **
403595 AAAATAGTAAAAA
1 AAAACAG-CAACC
403608 AAAACAGCAACC
1 AAAACAGCAACC
* *
403620 AAAACAGTAA-A
1 AAAACAGCAACC
*
403631 AAAACAAC-ACC
1 AAAACAGCAACC
403642 AAAACAGCAACC
1 AAAACAGCAACC
403654 AAAACA
1 AAAACA
403660 ATAATATAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
10 1 0.02
11 13 0.27
12 26 0.54
13 8 0.17
ACGTcount: A:0.66, C:0.23, G:0.06, T:0.04
Consensus pattern (12 bp):
AAAACAGCAACC
Found at i:403608 original size:23 final size:23
Alignment explanation
Indices: 403572--403645 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 23
403562 AAACAGTTAA
* *
403572 AAAATAGCACAAAAACAGCAACC
1 AAAATAGTAAAAAAACAGCAACC
403595 AAAATAGTAAAAAAAAACAGCAACC
1 AAAATAGT--AAAAAAACAGCAACC
* *
403620 AAAACAGTAAAAAAACAAC-ACC
1 AAAATAGTAAAAAAACAGCAACC
403642 AAAA
1 AAAA
403646 CAGCAACCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
22 7 0.16
23 17 0.38
25 21 0.47
ACGTcount: A:0.68, C:0.20, G:0.07, T:0.05
Consensus pattern (23 bp):
AAAATAGTAAAAAAACAGCAACC
Found at i:403626 original size:59 final size:60
Alignment explanation
Indices: 403471--403657 Score: 170
Period size: 60 Copynumber: 3.1 Consensus size: 60
403461 ACATCAAAAT
* * * * *
403471 AACCAAAATAATAACTAAAACAACAGCA-AAACAACA--ACAAAAAAAAGCAGCAAAAATAGC
1 AACCAAAATAACAACAAAAATAACAGCACCAA-AACAGTA-AAAAAAAAGCA-CAAAAACAGC
* * * * *
403531 AGCAAAAATAACAACAAAAATAACAGCATCAAAACAGTTAAAAAATAGCACAAAAACAGC
1 AACCAAAATAACAACAAAAATAACAGCACCAAAACAGTAAAAAAAAAGCACAAAAACAGC
** *
403591 AACCAAAATAGTAA-AAAAA-AACAGCAACCAAAACAGTAAAAAAACAA-CACCAAAACAGC
1 AACCAAAATAACAACAAAAATAACAGC-ACCAAAACAGTAAAAAAA-AAGCACAAAAACAGC
403650 AACCAAAA
1 AACCAAAA
403658 CAATAATATA
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
58 6 0.06
59 40 0.38
60 47 0.45
61 12 0.11
ACGTcount: A:0.66, C:0.20, G:0.07, T:0.07
Consensus pattern (60 bp):
AACCAAAATAACAACAAAAATAACAGCACCAAAACAGTAAAAAAAAAGCACAAAAACAGC
Found at i:403642 original size:22 final size:24
Alignment explanation
Indices: 403582--403648 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 24
403572 AAAATAGCAC
*
403582 AAAAACAGCAACCAAAATAGTAAAA
1 AAAAACAGCAACCAAAACAGT-AAA
403607 AAAAACAGCAACCAAAACAGT-AA
1 AAAAACAGCAACCAAAACAGTAAA
*
403630 AAAAACAAC-ACCAAAACAG
1 AAAAACAGCAACCAAAACAG
403649 CAACCAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.25
23 10 0.25
25 20 0.50
ACGTcount: A:0.67, C:0.21, G:0.07, T:0.04
Consensus pattern (24 bp):
AAAAACAGCAACCAAAACAGTAAA
Found at i:403951 original size:20 final size:20
Alignment explanation
Indices: 403926--403966 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
403916 TATGTAGGTA
403926 TGAGAATTTAGATTTCATCC
1 TGAGAATTTAGATTTCATCC
403946 TGAGAATTTAGATTTCATCC
1 TGAGAATTTAGATTTCATCC
403966 T
1 T
403967 AAATAATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TGAGAATTTAGATTTCATCC
Found at i:405877 original size:29 final size:30
Alignment explanation
Indices: 405848--405909 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
405838 TGTTTGTTTA
*
405848 TTTCTATAAATA-TTATTT-TTGTTATCTTAT
1 TTTC-ATAAATATTTATTTATT-TTATATTAT
*
405878 TTTCATAATTATTTATTTATTTTATATTAT
1 TTTCATAAATATTTATTTATTTTATATTAT
405908 TT
1 TT
405910 ATGTAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.21
30 20 0.71
31 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTCATAAATATTTATTTATTTTATATTAT
Found at i:418224 original size:20 final size:20
Alignment explanation
Indices: 418173--418232 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
418163 TTACTTGAAA
*
418173 TTTTA-ATATT-TTTTTAAT
1 TTTTATATATTATTTTCAAT
**
418191 TTTTATA-ACAATTTTCAAT
1 TTTTATATATTATTTTCAAT
*
418210 TTTTATATATTATTTTGAAT
1 TTTTATATATTATTTTCAAT
418230 TTT
1 TTT
418233 AAAATTTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 6 0.18
19 15 0.45
20 12 0.36
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATATATTATTTTCAAT
Found at i:418232 original size:19 final size:19
Alignment explanation
Indices: 418171--418233 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 19
418161 AATTACTTGA
*
418171 AATTTTA-ATATT-TTTTT
1 AATTTTATATATTATTTTC
**
418188 AATTTT-TATAACAATTTTC
1 AATTTTATAT-ATTATTTTC
*
418207 AATTTTTATATATTATTTTG
1 AA-TTTTATATATTATTTTC
418227 AATTTTA
1 AATTTTA
418234 AAATTTATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
17 8 0.23
18 1 0.03
19 11 0.31
20 12 0.34
21 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTATATATTATTTTC
Found at i:418399 original size:14 final size:14
Alignment explanation
Indices: 418382--418411 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
418372 TAATTTTTTT
*
418382 AATTTAAAGTTAAA
1 AATTTAAAATTAAA
418396 AATTTAAAATTAAA
1 AATTTAAAATTAAA
418410 AA
1 AA
418412 ACTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AATTTAAAATTAAA
Found at i:418447 original size:22 final size:23
Alignment explanation
Indices: 418401--418447 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
418391 TTAAAAATTT
* * *
418401 AAAATTAAAAAACTAAATTTTTA
1 AAAATAAAAAAACTAAATATCTA
418424 AAAATAAAAAAACTAAA-ATCTA
1 AAAATAAAAAAACTAAATATCTA
418446 AA
1 AA
418448 TTTTTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAATAAAAAAACTAAATATCTA
Found at i:421221 original size:2 final size:2
Alignment explanation
Indices: 421214--421241 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
421204 TTTTCTCTTA
421214 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
421242 TTTTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:423499 original size:2 final size:2
Alignment explanation
Indices: 423492--423523 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
423482 CATGTTTTCC
423492 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
423524 TCTAGTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.