Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 13 of 311
Found at i:3685233 original size:3 final size:3
Alignment explanation
Indices: 3685216--3685259 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
3685206 GGATGCAAAG
* * * *
3685216 GAA GAA GAT GCA GAA GAA GAA GTA GAA GAA GAA GAC GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3685260 TGAGTACGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.57, C:0.05, G:0.34, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:3686145 original size:8 final size:8
Alignment explanation
Indices: 3686134--3686166 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3686124 AAAAATAAAA
3686134 AAATTATG
1 AAATTATG
3686142 AAATTATG
1 AAATTATG
*
3686150 AATTTAT-
1 AAATTATG
3686157 AAATTATG
1 AAATTATG
3686165 AA
1 AA
3686167 TTTTCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (8 bp):
AAATTATG
Found at i:3686160 original size:15 final size:16
Alignment explanation
Indices: 3686137--3686169 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3686127 AATAAAAAAA
3686137 TTATGAAATTATGAAT
1 TTATGAAATTATGAAT
3686153 TTAT-AAATTATGAAT
1 TTATGAAATTATGAAT
3686168 TT
1 TT
3686170 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
TTATGAAATTATGAAT
Found at i:3686897 original size:18 final size:19
Alignment explanation
Indices: 3686862--3686897 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3686852 TTCCTTTTAA
3686862 TAATAAAAAAATTATTTTC
1 TAATAAAAAAATTATTTTC
*
3686881 TAATAAGAAAA-TATTTT
1 TAATAAAAAAATTATTTT
3686898 GTACTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TAATAAAAAAATTATTTTC
Found at i:3687721 original size:12 final size:12
Alignment explanation
Indices: 3687683--3687726 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3687673 ATGTATGTTT
3687683 AATAATATTGAA
1 AATAATATTGAA
* * *
3687695 AATTATTTTAAAA
1 AATAATATT-GAA
3687708 AATAATATTGAA
1 AATAATATTGAA
3687720 AATAATA
1 AATAATA
3687727 ATATTTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (12 bp):
AATAATATTGAA
Found at i:3687726 original size:15 final size:15
Alignment explanation
Indices: 3687682--3687731 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
3687672 TATGTATGTT
3687682 TAATAATATTGAAAA
1 TAATAATATTGAAAA
*
3687697 T--T-AT-TTTAAAA
1 TAATAATATTGAAAA
3687708 -AATAATATTGAAAA
1 TAATAATATTGAAAA
3687722 TAATAATATT
1 TAATAATATT
3687732 TTATATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
11 6 0.21
12 3 0.11
13 3 0.11
14 6 0.21
15 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (15 bp):
TAATAATATTGAAAA
Found at i:3689389 original size:22 final size:22
Alignment explanation
Indices: 3689361--3689407 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3689351 GTACAAATGA
3689361 ATGAAAGAGTTAATTAGATTTG
1 ATGAAAGAGTTAATTAGATTTG
3689383 ATGAAAGAGTTAATTAGATTTG
1 ATGAAAGAGTTAATTAGATTTG
3689405 ATG
1 ATG
3689408 TTTATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.36
Consensus pattern (22 bp):
ATGAAAGAGTTAATTAGATTTG
Found at i:3690478 original size:7 final size:6
Alignment explanation
Indices: 3690426--3690478 Score: 70
Period size: 6 Copynumber: 8.5 Consensus size: 6
3690416 ATAATTTAGT
* *
3690426 AAATAA AAATAA AAATAA AAATAA AAATCTTA AACTAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA
3690476 AAA
1 AAA
3690479 ACATATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 37 0.90
8 4 0.10
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:3690521 original size:18 final size:19
Alignment explanation
Indices: 3690498--3690548 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
3690488 TTTATACAAA
3690498 TAATTCGGTTAATTTAG-T
1 TAATTCGGTTAATTTAGAT
*
3690516 TAATTCAGG-TAA-TTCGAT
1 TAATTC-GGTTAATTTAGAT
*
3690534 TAATTCGATTAATTT
1 TAATTCGGTTAATTT
3690549 TTTTTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (19 bp):
TAATTCGGTTAATTTAGAT
Found at i:3701133 original size:25 final size:25
Alignment explanation
Indices: 3701099--3701151 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
3701089 TGAATTTTTT
3701099 CAGAATGAAGCTAGCAGAAAAAATA
1 CAGAATGAAGCTAGCAGAAAAAATA
*
3701124 CAGAATGAAGCTAGCAGAGAAAATA
1 CAGAATGAAGCTAGCAGAAAAAATA
3701149 CAG
1 CAG
3701152 CTTCTGTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.13, G:0.23, T:0.11
Consensus pattern (25 bp):
CAGAATGAAGCTAGCAGAAAAAATA
Found at i:3704348 original size:174 final size:175
Alignment explanation
Indices: 3704030--3704377 Score: 468
Period size: 174 Copynumber: 2.0 Consensus size: 175
3704020 CTTCAAGCAA
* * * * * *
3704030 GGAACAAAATAAAAGCATAAAGTGACCATACAGAATGTTTCCATTTAAAACGACCATCATAGCAA
1 GGAACAAAATAAAAGCATAAAGTGAACATACAGAATGTTTCCATCTAAAACAAACATCACAGAAA
* * * * * *
3704095 ACTGCAGTAACATCATCAGAAAGGCTGAATATTTCAAGGCCCATAACCCCAAACAGTGTGATGCT
66 ACTGCAGTAACATCATAAGAAAGACTAAATATTTCAAGGCCAAAAACCCCAAACAGTGTGATACT
* *
3704160 TACTATATTTTCAACATTGTGGGAGA-CCTAAATCCTCACCACAAT
131 TACTACAATTTCAACATTGTGGGA-ACCCTAAATCCTCACCACAAT
* *
3704205 GGAACGAAATAAAAGCATGAATGTGAACATACAGAATGTTTCC-TCTAAAA-AAACATCACAGAA
1 GGAACAAAATAAAAGCAT-AAAGTGAACATACAGAATGTTTCCATCTAAAACAAACATCACAGAA
* ** *
3704268 AACTGCAGTGACATCATAAGAAAGACTAAATATTTCAAGGCCAAAAATTCCAAACTGTGTGATAC
65 AACTGCAGTAACATCATAAGAAAGACTAAATATTTCAAGGCCAAAAACCCCAAACAGTGTGATAC
*
3704333 TTACTACAATTTCAACATTGTGGGAACCCTAGATCCTCACCACAA
130 TTACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAA
3704378 CGGACATGCA
Statistics
Matches: 150, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
173 1 0.01
174 104 0.69
175 23 0.15
176 22 0.15
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (175 bp):
GGAACAAAATAAAAGCATAAAGTGAACATACAGAATGTTTCCATCTAAAACAAACATCACAGAAA
ACTGCAGTAACATCATAAGAAAGACTAAATATTTCAAGGCCAAAAACCCCAAACAGTGTGATACT
TACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAAT
Found at i:3709967 original size:46 final size:46
Alignment explanation
Indices: 3709914--3710005 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
3709904 ATTTAAGATT
*
3709914 GAATTCCATGGGGGTTTCAGCTGGTTTACACCCCAACATCCCAACC
1 GAATTCCATGGGAGTTTCAGCTGGTTTACACCCCAACATCCCAACC
* *
3709960 GAATTCCATGGGAGTTTTAGCTGGTTTACACCCCAACATCCTAACC
1 GAATTCCATGGGAGTTTCAGCTGGTTTACACCCCAACATCCCAACC
3710006 TCAAATAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (46 bp):
GAATTCCATGGGAGTTTCAGCTGGTTTACACCCCAACATCCCAACC
Found at i:3722865 original size:16 final size:16
Alignment explanation
Indices: 3722831--3722884 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
3722821 AAGTGAAAAG
* * *
3722831 AAAATTAAAAATATGA
1 AAAAATAAAAAGATAA
* * *
3722847 AAAATTAAAGAGGTAA
1 AAAAATAAAAAGATAA
3722863 AAAAATAAAAAGATAA
1 AAAAATAAAAAGATAA
3722879 AAAAAT
1 AAAAAT
3722885 TTATATATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAAGATAA
Found at i:3730366 original size:43 final size:43
Alignment explanation
Indices: 3730299--3730412 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
3730289 TATTTTCGTC
* **
3730299 CACATGGTCA-GAGACACGGGCGTGTGTCTTAGTCGTGTGTGA
1 CACATGGTCAGGTGACACGACCGTGTGTCTTAGTCGTGTGTGA
** *
3730341 TGCATGGTCAGGTGACACGATCGTGTGTCTTAGTCGTGTGTGA
1 CACATGGTCAGGTGACACGACCGTGTGTCTTAGTCGTGTGTGA
*
3730384 CACACGGTCAGGTGACACGACCGTGTGTC
1 CACATGGTCAGGTGACACGACCGTGTGTC
3730413 CTCTGTGGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 8 0.13
43 54 0.87
ACGTcount: A:0.18, C:0.21, G:0.34, T:0.26
Consensus pattern (43 bp):
CACATGGTCAGGTGACACGACCGTGTGTCTTAGTCGTGTGTGA
Found at i:3734910 original size:43 final size:45
Alignment explanation
Indices: 3734863--3734960 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 45
3734853 GTTTATTATT
3734863 TATTTTAAAAAAACTTGAAATATATA-TTTGAAA-TATTTTTTAA
1 TATTTTAAAAAAACTTGAAATATATATTTTGAAATTATTTTTTAA
** * *
3734906 TATTTTTTAAAAATTTTAAATATATATTTTTGAAATTATTTTTTAA
1 TATTTTAAAAAAACTTGAAATATATA-TTTTGAAATTATTTTTTAA
* *
3734952 AAATTTAAA
1 TATTTTAAA
3734961 TATATTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 22 0.50
45 7 0.16
46 15 0.34
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (45 bp):
TATTTTAAAAAAACTTGAAATATATATTTTGAAATTATTTTTTAA
Found at i:3734966 original size:21 final size:21
Alignment explanation
Indices: 3734938--3734987 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3734928 TATATTTTTG
*
3734938 AAAT-TATTTTTTAAAAATTT
1 AAATATATTTTTTAAAAATAT
*
3734958 AAATATATTTTTTAATAATAT
1 AAATATATTTTTTAAAAATAT
3734979 AAA-ATATTT
1 AAATATATTT
3734988 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATATATTTTTTAAAAATAT
Found at i:3735072 original size:10 final size:10
Alignment explanation
Indices: 3735057--3735103 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
3735047 ATATTTTAAA
*
3735057 TTTTAAATAT
1 TTTTAAATTT
3735067 TTTT-AATTT
1 TTTTAAATTT
3735076 GTTTTATAATTT
1 -TTTTA-AATTT
3735088 TTTT-AATTT
1 TTTTAAATTT
3735097 TTTTAAA
1 TTTTAAA
3735104 ATGTATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 13 0.41
10 10 0.31
11 4 0.12
12 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:3735092 original size:21 final size:19
Alignment explanation
Indices: 3735057--3735103 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
3735047 ATATTTTAAA
3735057 TTTTAAATATTTTTAATTT
1 TTTTAAATATTTTTAATTT
*
3735076 GTTTTATAATTTTTTTAATTT
1 -TTTTA-AATATTTTTAATTT
3735097 TTTTAAA
1 TTTTAAA
3735104 ATGTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 13 0.52
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTAAATATTTTTAATTT
Found at i:3735195 original size:22 final size:23
Alignment explanation
Indices: 3735147--3735207 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
3735137 TTATTATTTG
**
3735147 TTTTATAATATTTTAAATGTATA
1 TTTTATAATATTTTAAAAATATA
3735170 TTTTA-AATATTTTAAAAATA-A
1 TTTTATAATATTTTAAAAATATA
3735191 TTTTTATAA-ATTATTAA
1 -TTTTATAATATT-TTAA
3735208 TTTTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.03
22 21 0.64
23 11 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAATATTTTAAAAATATA
Found at i:3738339 original size:17 final size:18
Alignment explanation
Indices: 3738306--3738339 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3738296 ATGTGGCCTG
*
3738306 CCCGTGTGGGCCTACATA
1 CCCGTGTGGGCCCACATA
3738324 CCCGTGT-GGCCCACAT
1 CCCGTGTGGGCCCACAT
3738340 GGCCCAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (18 bp):
CCCGTGTGGGCCCACATA
Found at i:3741516 original size:30 final size:30
Alignment explanation
Indices: 3741475--3741576 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
3741465 GTTTCTCTAG
*
3741475 GTGAAATGAACTCGAACCGCCTATG-TCAGA
1 GTGATATGAACTCGAACCGCCTATGTTC-GA
3741505 GTGATATGAACTCGAACCGCCTATGTTCGA
1 GTGATATGAACTCGAACCGCCTATGTTCGA
* * *
3741535 GTGATATGAACTCGAACTGCCAATGTTCGG
1 GTGATATGAACTCGAACCGCCTATGTTCGA
3741565 GTGATATGAACT
1 GTGATATGAACT
3741577 GTTCTTCAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 65 0.97
31 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (30 bp):
GTGATATGAACTCGAACCGCCTATGTTCGA
Found at i:3744262 original size:22 final size:20
Alignment explanation
Indices: 3744234--3744280 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
3744224 TATATATTTT
3744234 AAATAAAGTCATATTTTTTAAA
1 AAATAAA-TCAT-TTTTTTAAA
* *
3744256 AAATAAATCCTTTTTTTAAT
1 AAATAAATCATTTTTTTAAA
3744276 AAATA
1 AAATA
3744281 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 3 0.13
22 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATAAATCATTTTTTTAAA
Found at i:3744322 original size:20 final size:20
Alignment explanation
Indices: 3744306--3744344 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3744296 AAATTAATTC
*
3744306 AAATTTTACTTTTTTAAATA
1 AAATATTACTTTTTTAAATA
*
3744326 AAATATTATTTTTTTAAAT
1 AAATATTACTTTTTTAAAT
3744345 TTTAAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATATTACTTTTTTAAATA
Found at i:3744336 original size:25 final size:24
Alignment explanation
Indices: 3744265--3744337 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 24
3744255 AAAATAAATC
* *
3744265 CTTTTTTTAATAAATATTTTTTTA
1 CTTTTTTAAATAAATATTATTTTA
* *
3744289 -TTTTTTAAAATTAAT-TCAAATTTTA
1 CTTTTTT-AAATAAATAT--TATTTTA
3744314 CTTTTTTAAATAAAATATTATTTT
1 CTTTTTTAAAT-AAATATTATTTT
3744338 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
23 7 0.19
24 6 0.16
25 14 0.38
26 9 0.24
27 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
CTTTTTTAAATAAATATTATTTTA
Found at i:3744439 original size:31 final size:33
Alignment explanation
Indices: 3744386--3744453 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 33
3744376 CTTTAAAAAT
*
3744386 AATTAAAAAATCATAATTTAAAA-ATTATCTTTAA
1 AATTAAAAAA-CATAATTTAAAATA-TATATTTAA
3744420 AATTAAAAAA-AT-ATTTAAAATATATATTTAA
1 AATTAAAAAACATAATTTAAAATATATATTTAA
3744451 AAT
1 AAT
3744454 ATTATAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 19 0.59
32 3 0.09
34 10 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (33 bp):
AATTAAAAAACATAATTTAAAATATATATTTAA
Found at i:3744448 original size:13 final size:13
Alignment explanation
Indices: 3744430--3744455 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3744420 AATTAAAAAA
3744430 ATATTTAAAATAT
1 ATATTTAAAATAT
3744443 ATATTTAAAATAT
1 ATATTTAAAATAT
3744456 TATAAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:3744455 original size:11 final size:12
Alignment explanation
Indices: 3744371--3744452 Score: 52
Period size: 12 Copynumber: 7.1 Consensus size: 12
3744361 AAAAGGTTTG
*
3744371 AATATCTTTAAA
1 AATATATTTAAA
*
3744383 AATA-ATTAAAA
1 AATATATTTAAA
3744394 AATCATAATTTAAA
1 AAT-AT-ATTTAAA
*
3744408 AAT-TATCTTTAA
1 AATATAT-TTAAA
3744420 AAT-TA---AAA
1 AATATATTTAAA
3744428 AA-ATATTTAAA
1 AATATATTTAAA
3744439 ATATATATTTAAA
1 A-ATATATTTAAA
3744452 A
1 A
3744453 TATTATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
8 6 0.11
11 14 0.25
12 16 0.29
13 10 0.18
14 9 0.16
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATTTAAA
Found at i:3756711 original size:26 final size:25
Alignment explanation
Indices: 3756643--3756716 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
3756633 TTCATTCACG
* * *
3756643 TTACTTTTTACGATTCTTTGTCTTTT
1 TTACTTTTTAAG-TTCTTTTTATTTT
*
3756669 TT-CTTTTAAAGTT-TTTTTATTTAT
1 TTACTTTTTAAGTTCTTTTTATTT-T
3756693 TTACTTTTTAAGTTCTTTTTATTT
1 TTACTTTTTAAGTTCTTTTTATTT
3756717 GTCATTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 7 0.17
24 5 0.12
25 17 0.43
26 11 0.28
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.69
Consensus pattern (25 bp):
TTACTTTTTAAGTTCTTTTTATTTT
Found at i:3756756 original size:24 final size:25
Alignment explanation
Indices: 3756680--3756756 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 25
3756670 TCTTTTAAAG
* *
3756680 TTTTTTTATTTATTTACTTTTTAAGT
1 TTTTTTTATTTGTTTACTTATT-AGT
* * *
3756706 TCTTTTTATTTG-TCATTTATTTA-T
1 TTTTTTTATTTGTTTACTTA-TTAGT
*
3756730 TTTTTTTATTTGTTTA-TTATTGGT
1 TTTTTTTATTTGTTTACTTATTAGT
3756754 TTT
1 TTT
3756757 ATAAAATCTG
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
23 2 0.05
24 19 0.47
25 7 0.17
26 12 0.30
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (25 bp):
TTTTTTTATTTGTTTACTTATTAGT
Found at i:3756819 original size:21 final size:20
Alignment explanation
Indices: 3756793--3756861 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
3756783 TGTTTTATAA
3756793 TATTTTT-AATTTTAAATAT
1 TATTTTTAAATTTTAAATAT
*
3756812 ATATTTTTAAAATTTAAATAT
1 -TATTTTTAAATTTTAAATAT
*
3756833 TATTTTAAAATTTTAAATAT
1 TATTTTTAAATTTTAAATAT
3756853 TATTTTTAA
1 TATTTTTAA
3756862 TAATATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 33 0.75
21 11 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTTAAATTTTAAATAT
Found at i:3756893 original size:16 final size:16
Alignment explanation
Indices: 3756849--3756900 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3756839 AAAATTTTAA
3756849 ATATTATTTTTAATAAT
1 ATATTATTTTTAA-AAT
** **
3756866 ATAAAACATTTAAAAT
1 ATATTATTTTTAAAAT
3756882 ATATTATTTTTAAAGAT
1 ATATTATTTTTAAA-AT
3756899 AT
1 AT
3756901 GACCTTTCAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTATTTTTAAAAT
Found at i:3757068 original size:25 final size:25
Alignment explanation
Indices: 3757025--3757073 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3757015 TTTTTAAAGA
*
3757025 TATTTAAATATTTTTAAAAAAATAC
1 TATTTAAATATTTTAAAAAAAATAC
3757050 TATTTAAA-ATTTTAAAAAATAATA
1 TATTTAAATATTTTAAAAAA-AATA
3757074 TTTTATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTTAAATATTTTAAAAAAAATAC
Found at i:3757069 original size:22 final size:25
Alignment explanation
Indices: 3757024--3757076 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
3757014 ATTTTTAAAG
3757024 ATATTTAAATATTTTTAAAAAAATA
1 ATATTTAAATATTTTTAAAAAAATA
*
3757049 CTATTTAAA-A-TTTT-AAAAAATA
1 ATATTTAAATATTTTTAAAAAAATA
3757071 ATATTT
1 ATATTT
3757077 TATTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 13 0.50
23 4 0.15
24 1 0.04
25 8 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTAAATATTTTTAAAAAAATA
Found at i:3757179 original size:21 final size:20
Alignment explanation
Indices: 3757155--3757207 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
3757145 TGATTTTTTT
3757155 AAATATATATTAAAAAAGTAA
1 AAATATATATTAAAAAA-TAA
* * *
3757176 AAATTTATATTAGAAAATTA
1 AAATATATATTAAAAAATAA
3757196 AAATATATATTA
1 AAATATATATTA
3757208 CAATTAGTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AAATATATATTAAAAAATAA
Found at i:3761902 original size:52 final size:51
Alignment explanation
Indices: 3761830--3762032 Score: 169
Period size: 54 Copynumber: 3.8 Consensus size: 51
3761820 ATATCATACC
* * * * *
3761830 GATGCCATATCCCGGATATGGTCTTACACGGGAGCACTTATCATTATTCACA
1 GATGCCATAGCCCAGCTATGGTCTTATACGGGATCACTTATCATTATTC-CA
*
3761882 GATGCCATAGCCCAGCTATGGTCTTATAC-GGATCACTTGTATCACATTAATCC-
1 GATGCCATAGCCCAGCTATGGTCTTATACGGGATCAC-T-TAT--CATTATTCCA
* * * * *
3761935 GAAGCCATAGCCCAGCTCTGGTCTTATACGGAAATCACTTATCTTTTGTTTTCCA
1 GATGCCATAGCCCAGCTATGGTCTTATACGG-GATCACTTATC--AT-TATTCCA
* * *
3761990 -ATGCCATAGCCCAGCTATGGTATTATATGGGTATCGCTTATCA
1 GATGCCATAGCCCAGCTATGGTCTTATACGGG-ATCACTTATCA
3762033 CTTGTTGCCA
Statistics
Matches: 121, Mismatches: 19, Indels: 22
0.75 0.12 0.14
Matches are distributed among these distances:
51 7 0.06
52 26 0.21
53 34 0.28
54 42 0.35
55 12 0.10
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (51 bp):
GATGCCATAGCCCAGCTATGGTCTTATACGGGATCACTTATCATTATTCCA
Found at i:3764043 original size:21 final size:22
Alignment explanation
Indices: 3764004--3764045 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3763994 AACCACCAAA
**
3764004 TAAATATTAATTTTTAAAATTT
1 TAAATATTAATTTGAAAAATTT
3764026 TAAATA-TAATTTGAAAAATT
1 TAAATATTAATTTGAAAAATT
3764046 AACAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAATATTAATTTGAAAAATTT
Found at i:3764070 original size:23 final size:23
Alignment explanation
Indices: 3764044--3764108 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 23
3764034 ATTTGAAAAA
3764044 TTAACAATTTTAAAAAATTATAT
1 TTAACAATTTTAAAAAATTATAT
**
3764067 TTAA-AATTAAAAAAAATT-TAAT
1 TTAACAATTTTAAAAAATTAT-AT
* *
3764089 TTTAC-A-TTTAAAATATTATA
1 TTAACAATTTTAAAAAATTATA
3764109 AAACAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 10 0.30
22 19 0.58
23 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAACAATTTTAAAAAATTATAT
Found at i:3764224 original size:11 final size:12
Alignment explanation
Indices: 3764194--3764223 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3764184 ATATTTAAGA
3764194 TTAAAAATATAT
1 TTAAAAATATAT
3764206 TTAAAAATATAT
1 TTAAAAATATAT
3764218 TTAAAA
1 TTAAAA
3764224 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAAAAATATAT
Found at i:3764313 original size:11 final size:11
Alignment explanation
Indices: 3764297--3764325 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3764287 AAATAAAATA
3764297 AAATAAAGGAC
1 AAATAAAGGAC
3764308 AAATAAAGGAC
1 AAATAAAGGAC
3764319 AAATAAA
1 AAATAAA
3764326 AAACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (11 bp):
AAATAAAGGAC
Found at i:3764351 original size:24 final size:25
Alignment explanation
Indices: 3764319--3764366 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3764309 AATAAAGGAC
*
3764319 AAAT-AAAAAACATAAAAATTAAAT
1 AAATAAAAAAACATAAAAAGTAAAT
*
3764343 AAATAAAAAAACTTAAAAAGTAAA
1 AAATAAAAAAACATAAAAAGTAAA
3764367 AAAAATTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (25 bp):
AAATAAAAAAACATAAAAAGTAAAT
Found at i:3764358 original size:18 final size:16
Alignment explanation
Indices: 3764322--3764370 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3764312 AAAGGACAAA
* *
3764322 TAAAAAACATAAAAAT
1 TAAAAAATAAAAAAAT
3764338 TAAATAAATAAAAAAACT
1 TAAA-AAATAAAAAAA-T
*
3764356 TAAAAAGTAAAAAAA
1 TAAAAAATAAAAAAA
3764371 ATTACAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 19 0.68
18 5 0.18
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (16 bp):
TAAAAAATAAAAAAAT
Found at i:3764379 original size:17 final size:17
Alignment explanation
Indices: 3764332--3764379 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3764322 TAAAAAACAT
*
3764332 AAAAATTAAATAAATAAA
1 AAAAATTAAA-AAGTAAA
*
3764350 AAAACTTAAAAAGTAAA
1 AAAAATTAAAAAGTAAA
*
3764367 AAAAATTACAAAG
1 AAAAATTAAAAAG
3764380 AACCAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAAATTAAAAAGTAAA
Found at i:3765028 original size:19 final size:20
Alignment explanation
Indices: 3765004--3765051 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3764994 ACTCAACAGT
*
3765004 GAAAAAAAATA-CTGAAAAC
1 GAAAAAAAATAGCTAAAAAC
3765023 GAAAAAAAA-AGCTAAAAAC
1 GAAAAAAAATAGCTAAAAAC
3765042 -AAAAAAAATA
1 GAAAAAAAATA
3765052 AAAAAATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (20 bp):
GAAAAAAAATAGCTAAAAAC
Found at i:3765257 original size:22 final size:22
Alignment explanation
Indices: 3765189--3765258 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
3765179 ACAAAGAAGG
* *
3765189 AGAAG-AAGAAAAAGAAAAGAA
1 AGAAGAAAGAAAAAGAAAGGGA
*
3765210 TGAGAAGAAAG--AAAGAAGAGCAGA
1 --AGAAGAAAGAAAAAGAA-AG-GGA
3765234 AGAAGAAAGAAAAAGAAAGGGA
1 AGAAGAAAGAAAAAGAAAGGGA
3765256 AGA
1 AGA
3765259 GGAGGAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
22 20 0.53
23 8 0.21
24 10 0.26
ACGTcount: A:0.67, C:0.01, G:0.30, T:0.01
Consensus pattern (22 bp):
AGAAGAAAGAAAAAGAAAGGGA
Found at i:3765979 original size:12 final size:13
Alignment explanation
Indices: 3765964--3766024 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
3765954 ATTTTTTGCT
3765964 AAAATAATATA-A
1 AAAATAATATACA
*
3765976 AAAATAAAATACA
1 AAAATAATATACA
*
3765989 AAAATAATATATTTTA
1 AAAATAATATA---CA
*
3766005 AAAATAATATACG
1 AAAATAATATACA
3766018 AAAATAA
1 AAAATAA
3766025 AAAATACGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.25
13 18 0.45
16 12 0.30
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAATAATATACA
Found at i:3766199 original size:150 final size:151
Alignment explanation
Indices: 3765816--3767046 Score: 1742
Period size: 150 Copynumber: 8.2 Consensus size: 151
3765806 GAGTTTTTTG
* * *
3765816 CTAAAATAATATAAA-AAATAAAATATGAAAATAGTATATTTT-AAAAA-AA-ATCCGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT-A
* * * *
3765877 AAAAATACGAACAAGGTGCCAAAGTCAGGGTTATTTATTAAATTAATAT-AAAAAA-ACTTAAAT
65 AAAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAAACACTTAAAT
* * *
3765940 AATACATTTGAAACATTTTTTG
130 AATACATTTGAAACATTATGTA
* *
3765962 CTAAAATAATATAAA-AAATAAAATACAAAAATAATATATTTT-AAAAATAATATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
*
3766025 AAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAA-AAATATAAAAAAACACTTAAATA
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAAACACTTAAATA
*
3766089 ATACATTTAAAACATTATGTA
131 ATACATTTGAAACATTATGTA
* *
3766110 TTAAAATAATATAAAGAAATAAAATATGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
* * *
3766175 AAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTAAGTA
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAAACACTTAAATA
* * *
3766240 ATACATTTGAAACATTTTTTG
131 ATACATTTGAAACATTATGTA
* * * * *
3766261 CTAAAATAATATAAAAAAATAAAATA-AAAAATAAAATATTTTAAAAAATAATATATGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
*
3766325 AAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAGA-AAATAT-AAAAAACACTTAAAT
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAA-ATAAATATAAAAAAACACTTAAAT
*
3766388 AATACATTTGAAATATTATGTA
130 AATACATTTGAAACATTATGTA
*
3766410 CTAAAATAATATAAAGAAATAAAATATGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT-A
* * * **
3766475 AAAAATGCGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAACACTTACGT
65 AAAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAAACACTTAAAT
* *
3766539 AATACATTTGAAACATTTTTTA
130 AATACATTTGAAACATTATGTA
* *
3766561 CTAAAATAATATAAA-AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACAAAAAT-A
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
* *
3766624 AAAATACGAATAAAGTGCTAAAATCAGGATTATTTATTAAGA-AAATATAAAAAAACACTTAAAT
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAA-ATAAATATAAAAAAACACTTAAAT
3766688 AATACATTTGAAACATTATGTA
130 AATACATTTGAAACATTATGTA
3766710 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
* * *
3766775 AAAA-ATGAATAAAGTGCTAAAATCAGGATTATTTATTAAGA-AAATATAAAAAAACACTTAAAT
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAA-ATAAATATAAAAAAACACTTAAAT
3766838 AATACATTTGAAACATTATGTA
130 AATACATTTGAAACATTATGTA
* * * *
3766860 CTAAAATAATGTAAAGGAATAAAATAGGAAAATAATATATTTTAAAAAATAAGATACAAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT-A
* * * * * * * *
3766925 AAAAATACGAAGAAAATGCCAAAATTAGGATTTTTTATTAAATTAATATAAAAAAATACTTACAT
65 AAAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAAACACTTAAAT
* * *
3766990 AATACATTTGAAACATTTTTTG
130 AATACATTTGAAACATTATGTA
*
3767012 CTAAAATAATATAAATAAATAAAATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAA
3767047 AAAATACGAA
Statistics
Matches: 979, Mismatches: 88, Indels: 30
0.89 0.08 0.03
Matches are distributed among these distances:
146 49 0.05
147 47 0.05
148 91 0.09
149 131 0.13
150 397 0.41
151 166 0.17
152 98 0.10
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (151 bp):
CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAAACACTTAAATA
ATACATTTGAAACATTATGTA
Found at i:3766295 original size:12 final size:12
Alignment explanation
Indices: 3766263--3766298 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3766253 ATTTTTTGCT
*
3766263 AAAATAATATAAA
1 AAAATAAAAT-AA
3766276 AAAATAAAATAA
1 AAAATAAAATAA
3766288 AAAATAAAATA
1 AAAATAAAATA
3766299 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:3766296 original size:30 final size:31
Alignment explanation
Indices: 3766262--3766330 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
3766252 CATTTTTTGC
3766262 TAAAATAATATAAAAAAATAAAATA-AAAAA
1 TAAAATAATATAAAAAAATAAAATATAAAAA
* * * *
3766292 TAAAAT-ATTTTAAAAAATAATATATGAAAA
1 TAAAATAATATAAAAAAATAAAATATAAAAA
3766322 TAAAA-AATA
1 TAAAATAATA
3766331 CGAATAAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (31 bp):
TAAAATAATATAAAAAAATAAAATATAAAAA
Found at i:3766298 original size:17 final size:17
Alignment explanation
Indices: 3766262--3766330 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
3766252 CATTTTTTGC
3766262 TAAAATAATATAAA-AAAA
1 TAAAATAA-A-AAATAAAA
3766280 TAAAATAAAAAATAAAA
1 TAAAATAAAAAATAAAA
***
3766297 TATTTTAAAAAATAATATA
1 TAAAATAAAAAATAA-A-A
3766316 TGAAAATAAAAAATA
1 T-AAAATAAAAAATA
3766331 CGAATAAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.07
17 17 0.41
18 9 0.22
19 2 0.05
20 10 0.24
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (17 bp):
TAAAATAAAAAATAAAA
Found at i:3766622 original size:13 final size:13
Alignment explanation
Indices: 3766563--3766624 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
3766553 ATTTTTTACT
3766563 AAAATAATATA-A
1 AAAATAATATACA
* *
3766575 AAAATAAAATACG
1 AAAATAATATACA
*
3766588 AAAATAATATATTTTAA
1 AAAATAATATA----CA
3766605 AAAATAATATACA
1 AAAATAATATACA
3766618 AAAATAA
1 AAAATAA
3766625 AAATACGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
12 10 0.26
13 18 0.46
17 11 0.28
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAATAATATACA
Found at i:3766883 original size:450 final size:450
Alignment explanation
Indices: 3765816--3767345 Score: 2113
Period size: 450 Copynumber: 3.5 Consensus size: 450
3765806 GAGTTTTTTG
* * *
3765816 CTAAAATAATATAAA-AAATAAAATATGAAAATAGTATATTTT-AAAAA-AA-ATCCGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT-A
* * * *
3765877 AAAAATACGAACAAGGTGCCAAAGTCAGGGTTATTTATTAAATTAATATAAAAAA-ACTTAAATA
65 AAAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAACACTTAAATA
* * * *
3765941 ATACATTTGAAACATTTTTTGCTAAAATAATATAAA-AAATAAAATACAAAAATAATATATTTT-
130 ATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTA
* * * *
3766004 AAAAATAATATACGAAAAT-AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAA-A
195 AAAAATAAGATACGAAAATAAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATT
* * * * *
3766067 AATATAAAAAAACACTTAAATAATACATTTAAAACATTATGTATTAAAATAATATAAAGAAATAA
260 AATATAAAAAAACACTTACATAATACATTTGAAACATTTTTTACTAAAATAATATAAAGAAATAA
* * *
3766132 AATATGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAAATACGAAGAAAGTGCCAAA
325 AATACGAAAATAATATATTTTAAAAAATAA-ATAC-AAAAT-AAAAATACGAATAAAGTGCTAAA
* * * * *
3766197 ATCAGGGTTATTTATTAA-ATTAATATAAAAAAACACTTAAGTAATACATTTGAAACATTTTTTG
387 ATCAGGGTTATTTATTAAGA-AAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTA
* * * * *
3766261 CTAAAATAATATAAAAAAATAAAATA-AAAAATAAAATATTTTAAAAAATAATATATGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
*
3766325 AAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAGA-AAATATAAAAAACACTTAAATA
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAA-ATAAATATAAAAAACACTTAAATA
* *
3766389 ATACATTTGAAATATTATGTACTAAAATAATATAAAGAAATAAAATATGAAAATAATATATTTTA
130 ATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTA
*
3766454 AAAAATAAGATACGAAAATAAAAAAATGCGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATT
195 AAAAATAAGATACGAAAATAAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATT
*
3766519 AATAT-AAAAAACACTTACGTAATACATTTGAAACATTTTTTACTAAAATAATATAAA-AAATAA
260 AATATAAAAAAACACTTACATAATACATTTGAAACATTTTTTACTAAAATAATATAAAGAAATAA
3766582 AATACGAAAATAATATATTTTAAAAAATAATATACAAAAATAAAAATACGAATAAAGTGCTAAAA
325 AATACGAAAATAATATATTTTAAAAAATAA-ATAC-AAAATAAAAATACGAATAAAGTGCTAAAA
*
3766647 TCAGGATTATTTATTAAGAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTA
388 TCAGGGTTATTTATTAAGAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTA
3766710 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
* * *
3766775 AAAA-ATGAATAAAGTGCTAAAATCAGGATTATTTATTAAGA-AAATATAAAAAAACACTTAAAT
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAA-ATAAATAT-AAAAAACACTTAAAT
* * *
3766838 AATACATTTGAAACATTATGTACTAAAATAATGTAAAGGAATAAAATAGGAAAATAATATATTTT
129 AATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTT
* * * * *
3766903 AAAAAATAAGATACAAAAATAAAAAAATACGAAGAAAATGCCAAAATTAGGATTTTTTATTAAAT
194 AAAAAATAAGATACGAAAATAAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAAT
* * *
3766968 TAATATAAAAAAATACTTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAATAAATA
259 TAATATAAAAAAACACTTACATAATACATTTGAAACATTTTTTACTAAAATAATATAAAGAAATA
3767033 AAATACG--------------------A-AAAT-----A-AAAAATACGAATAAAGTGCTAAAAT
324 AAATACGAAAATAATATATTTTAAAAAATAAATACAAAATAAAAATACGAATAAAGTGCTAAAAT
3767071 CAGGGTTATTTATTAAGAAAATAT-AAAAAACACTTAAATAATACATTTGAAACATTATGTA
389 CAGGGTTATTTATTAAGAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTA
3767132 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
1 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
* * *
3767197 AAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTACATAA
66 AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAACACTTAAATAA
* * * *
3767262 TACATTTGAAACATTTTTTGCTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAA
131 TACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAA
*
3767327 AAAATAATATACGAAAATA
196 AAAATAAGATACGAAAATA
3767346 TTTTACTTAT
Statistics
Matches: 994, Mismatches: 74, Indels: 57
0.88 0.07 0.05
Matches are distributed among these distances:
422 198 0.20
423 84 0.08
424 1 0.00
430 2 0.00
431 2 0.00
432 1 0.00
445 28 0.03
446 15 0.02
447 51 0.05
448 50 0.05
449 168 0.17
450 242 0.24
451 135 0.14
452 17 0.02
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.29
Consensus pattern (450 bp):
CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAA
AAAATACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATAAATATAAAAAACACTTAAATAA
TACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAA
AAAATAAGATACGAAAATAAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATTA
ATATAAAAAAACACTTACATAATACATTTGAAACATTTTTTACTAAAATAATATAAAGAAATAAA
ATACGAAAATAATATATTTTAAAAAATAAATACAAAATAAAAATACGAATAAAGTGCTAAAATCA
GGGTTATTTATTAAGAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTA
Found at i:3767069 original size:26 final size:26
Alignment explanation
Indices: 3767010--3767070 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
3767000 AAACATTTTT
3767010 TGCTAAAATAATATAAATAAATAAAA
1 TGCTAAAATAATATAAATAAATAAAA
* * *
3767036 TACGAAAATAA-A-AAATACGAATAAAG
1 TGCTAAAATAATATAAATA--AATAAAA
3767062 TGCTAAAAT
1 TGCTAAAAT
3767071 CAGGGTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 5 0.18
25 1 0.04
26 22 0.79
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (26 bp):
TGCTAAAATAATATAAATAAATAAAA
Found at i:3767136 original size:120 final size:120
Alignment explanation
Indices: 3766902--3767166 Score: 354
Period size: 120 Copynumber: 2.2 Consensus size: 120
3766892 TAATATATTT
* * * *
3766902 TAAAAAATAAGATACAAAAATAAAAAAATACGAAGAAAATGCCAAAATTAGGATTTTTTATTAAA
1 TAAAAAATAAAATACGAAAAT-AAAAAATACGAAGAAAATGCCAAAATCAGGATTATTTATTAAA
* * * * * *
3766967 TTAATATAAAAAAATACTTACATAATACATTTGAAACATTTTTTGCTAAAATAATA
65 TAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATA
* * * *
3767023 TAAATAAATAAAATACGAAAATAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAG
1 TAAA-AAATAAAATACGAAAATAAAAAATACGAAGAAAATGCCAAAATCAGGATTATTTATTAA-
3767088 A-AAATAT-AAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATA
64 ATAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATA
3767143 TAAAGAAATAAAATACGAAAATAA
1 TAAA-AAATAAAATACGAAAATAA
3767167 TATATTTTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
120 66 0.52
121 45 0.35
122 16 0.13
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (120 bp):
TAAAAAATAAAATACGAAAATAAAAAATACGAAGAAAATGCCAAAATCAGGATTATTTATTAAAT
AAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATA
Found at i:3767193 original size:150 final size:150
Alignment explanation
Indices: 3767023--3767345 Score: 531
Period size: 150 Copynumber: 2.1 Consensus size: 150
3767013 TAAAATAATA
* *
3767023 TAAATAAATAAAATACGAAAATAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAG
1 TAAA-AAATAAAATACGAAAATAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAA-
*
3767088 A-AAATATAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAAT
64 ATAAATATAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAAT
3767152 AAAATACGAAAATAATATATTT
129 AAAATACGAAAATAATATATTT
*
3767174 TAAAAAATAAGATACGAAAATAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAAT
1 TAAAAAATAAAATACGAAAATAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAAT
* * * * *
3767239 TAATATAAAAAACACTTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAAATAA
66 AAATATAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAA
3767304 AATACGAAAATAATATATTT
131 AATACGAAAATAATATATTT
*
3767324 TAAAAAATAATATACGAAAATA
1 TAAAAAATAAAATACGAAAATA
3767346 TTTTACTTAT
Statistics
Matches: 161, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
149 1 0.01
150 156 0.97
151 4 0.02
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (150 bp):
TAAAAAATAAAATACGAAAATAAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAAT
AAATATAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAA
AATACGAAAATAATATATTT
Found at i:3769907 original size:17 final size:17
Alignment explanation
Indices: 3769887--3769925 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
3769877 AATACATTAC
3769887 AACATTAATCT-AATTGG
1 AACATTAAT-TAAATTGG
3769904 AACATTAATTAAATTGG
1 AACATTAATTAAATTGG
3769921 AACAT
1 AACAT
3769926 ACTATTACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (17 bp):
AACATTAATTAAATTGG
Found at i:3774474 original size:9 final size:9
Alignment explanation
Indices: 3774460--3774488 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3774450 TTGAAAGATT
3774460 AAGTGCCAA
1 AAGTGCCAA
3774469 AAGTGCCAA
1 AAGTGCCAA
3774478 AAGTGCCAA
1 AAGTGCCAA
3774487 AA
1 AA
3774489 ATGGTACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (9 bp):
AAGTGCCAA
Found at i:3774861 original size:20 final size:19
Alignment explanation
Indices: 3774838--3774883 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3774828 TTCTTTCCTC
**
3774838 CTCCTTCTTTTTCTTCTCTT
1 CTCCTTCTTTCCCTT-TCTT
3774858 CTCCTTTCTTTCCCTTTCTT
1 CTCC-TTCTTTCCCTTTCTT
3774878 CTCCTT
1 CTCCTT
3774884 GTTGCTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 12 0.52
21 9 0.39
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (19 bp):
CTCCTTCTTTCCCTTTCTT
Found at i:3775036 original size:18 final size:18
Alignment explanation
Indices: 3775013--3775056 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
3775003 TATCTTTTTA
3775013 TTTTTTTTGTTTTCAG-T
1 TTTTTTTTGTTTTCAGAT
3775030 TTTTTTTTGTTTTCAGCAT
1 TTTTTTTTGTTTTCAG-AT
3775049 TTTTTTTT
1 TTTTTTTT
3775057 CACTATTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 16 0.64
19 9 0.36
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTTTTTTGTTTTCAGAT
Found at i:3791737 original size:38 final size:40
Alignment explanation
Indices: 3791693--3791856 Score: 151
Period size: 39 Copynumber: 4.2 Consensus size: 40
3791683 TGAAACCGAT
* *
3791693 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-TATAA
1 TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
* * *
3791731 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
* * * *
3791770 TTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGATATAA
1 TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
* ** *
3791809 TTCCAGCAC-ATAGCCTGC-GGACCCTAAGTCCGGATATAA
1 TACCAGCACGA-AGCCTGCGGGACTTTAAGCCCGGATATAA
*
3791848 TTCCAGCAC
1 TACCAGCAC
3791857 ATAACCTGTG
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 20 0.19
39 88 0.81
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (40 bp):
TACCAGCACGAAGCCTGCGGGACTTTAAGCCCGGATATAA
Found at i:3791808 original size:78 final size:78
Alignment explanation
Indices: 3791722--3791885 Score: 181
Period size: 78 Copynumber: 2.1 Consensus size: 78
3791712 GAATTTAAAC
* * * * * *
3791722 CCGG-TATAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAGCACGTAGC
1 CCGGATATAATACCAGCAC-ATAGCCTGC-GGACCCTAAGCCCGGACATAATTCCAGCACATAAC
*
3791784 CTGCGGACCTTAAGT
64 CTGCGGACCCTAAGT
* * *
3791799 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACATAACCT
1 CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAACCT
*
3791864 GTGGACCCTAAGT
66 GCGGACCCTAAGT
*
3791877 CCAGATATA
1 CCGGATATA
3791886 CATCACTGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.11
78 64 0.89
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (78 bp):
CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAACCT
GCGGACCCTAAGT
Found at i:3791857 original size:39 final size:39
Alignment explanation
Indices: 3791760--3791885 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
3791750 GGACTTTAGC
* * * *
3791760 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
3791799 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
* *
3791838 CCGGATATAATTCCAGCACATAACCTGTGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
3791877 CCAGATATA
1 CCGGATATA
3791886 CATCACTGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:3816831 original size:60 final size:60
Alignment explanation
Indices: 3816739--3816853 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
3816729 TATCTTTTAA
* * * *
3816739 TTTTTTAGAGATAGGACTAAATTGATAGATTTTGTAAATATTAAGGG-TCAAATTTATTAT
1 TTTTTTAGAGATAGAACTAAAATGACAAATTTTGTAAATATTAAGGGCT-AAATTTATTAT
3816799 TTTTTTAGA-ATTAGAACTAAAATGACAAATTTTGTAAATATTAAGGGCTAAATTT
1 TTTTTTAGAGA-TAGAACTAAAATGACAAATTTTGTAAATATTAAGGGCTAAATTT
3816854 GTTGAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 1 0.02
60 47 0.96
61 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (60 bp):
TTTTTTAGAGATAGAACTAAAATGACAAATTTTGTAAATATTAAGGGCTAAATTTATTAT
Found at i:3818729 original size:58 final size:58
Alignment explanation
Indices: 3818589--3818730 Score: 162
Period size: 58 Copynumber: 2.4 Consensus size: 58
3818579 GAATCTTTTG
* * *
3818589 GGCTCTCGATC-AAGGTGAGGTATATCTTCAACACTCGGGTCCCTCCGTGAACCATTCA
1 GGCTCTCGA-CGAAGGTGAGGCATATCTTCAACACTCGGGCCCCTCCATGAACCATTCA
* * * * * *
3818647 GGCTCTCAATGAAAGTGAGACATATCTTCAACATTCGGGCCCCTCCATGAACCGTTCTA
1 GGCTCTCGACGAAGGTGAGGCATATCTTCAACACTCGGGCCCCTCCATGAACCATTC-A
*
3818706 -GCTCTCGACGAAGGTAAGGCATATC
1 GGCTCTCGACGAAGGTGAGGCATATC
3818731 ATCTTCATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
58 67 0.99
59 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (58 bp):
GGCTCTCGACGAAGGTGAGGCATATCTTCAACACTCGGGCCCCTCCATGAACCATTCA
Found at i:3818825 original size:18 final size:19
Alignment explanation
Indices: 3818792--3818832 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3818782 CACACACACT
3818792 TTATTTCTCTAGATCAACA
1 TTATTTCTCTAGATCAACA
3818811 GTTATTT-TC-AGATCAACA
1 -TTATTTCTCTAGATCAACA
3818829 TTAT
1 TTAT
3818833 AATACCACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 2 0.10
20 6 0.29
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (19 bp):
TTATTTCTCTAGATCAACA
Found at i:3820625 original size:29 final size:26
Alignment explanation
Indices: 3820574--3820627 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3820564 GCTCACTGGA
3820574 GTTTTCTTTTAATTTTTAATTCAGTG
1 GTTTTCTTTTAATTTTTAATTCAGTG
*
3820600 GTTTTTTTTTAAATTTTTTAACTTCAGT
1 GTTTTCTTTT-AA-TTTTTAA-TTCAGT
3820628 TTGATTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 7 0.29
29 6 0.25
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.63
Consensus pattern (26 bp):
GTTTTCTTTTAATTTTTAATTCAGTG
Found at i:3821884 original size:44 final size:44
Alignment explanation
Indices: 3821834--3821929 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
3821824 GTAGGTCAAA
* * * *
3821834 TAATATTAAAATAACTTACTCTAA-TTAGAGTTTAAGTGGGTAAC
1 TAATATTAAAATAACCTACACTAATTTA-AGTTTAAGTGAGAAAC
3821878 TAATATTAAAATAACCTACACTAATTTAAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATTTAAGTTTAAGTGAGAAAC
*
3821922 TAAAATTA
1 TAATATTA
3821930 GAGTTTAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.34
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATTTAAGTTTAAGTGAGAAAC
Found at i:3822435 original size:40 final size:40
Alignment explanation
Indices: 3822380--3822499 Score: 204
Period size: 40 Copynumber: 3.0 Consensus size: 40
3822370 TTTGCCTCTA
* * *
3822380 ATGTTAGGTCATTTAACACGTTATCAAAATATCAAAATTT
1 ATGTTACGTCATTTAACATGTTATCAAAATGTCAAAATTT
3822420 ATGTTACGTCATTTAACATGTTATCAAAATGTCAAAATTT
1 ATGTTACGTCATTTAACATGTTATCAAAATGTCAAAATTT
*
3822460 ATGTTACATCATTTAACATGTTATCAAAATGTCAAAATTT
1 ATGTTACGTCATTTAACATGTTATCAAAATGTCAAAATTT
3822500 TATCATGTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (40 bp):
ATGTTACGTCATTTAACATGTTATCAAAATGTCAAAATTT
Found at i:3825424 original size:46 final size:46
Alignment explanation
Indices: 3825372--3825595 Score: 249
Period size: 46 Copynumber: 4.8 Consensus size: 46
3825362 GATATTTGGG
*
3825372 CATCCGACCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
* *
3825418 CATCCGAACTCGTTGAGTTGAGTCTTG-GTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTC-CGAGTTCACTTATGGATGCAAA
* * * * *
3825464 CGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-AG-TGTAACTA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A
* *
3825509 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAA
1 --CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
** * *
3825557 CGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3825596 GCGGGTTACA
Statistics
Matches: 147, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
43 3 0.02
44 1 0.01
45 4 0.03
46 102 0.69
47 30 0.20
48 3 0.02
49 1 0.01
50 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
Found at i:3825542 original size:93 final size:93
Alignment explanation
Indices: 3825418--3825588 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3825408 TGGATGCAAA
*** *
3825418 CATCCGAACTCGTTGAGTTGAGTCTTGGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
3825483 GAGTCCGAGTTCGTGAAGTGTAACTAGG
66 GAGTCCGAGTTCGTGAAGTGTAACTAGG
*
3825511 CATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
3825576 GAGTCCGAGTTCG
66 GAGTCCGAGTTCG
3825589 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAAGTGTAACTAGG
Found at i:3834602 original size:22 final size:24
Alignment explanation
Indices: 3834548--3834602 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
3834538 CATATAACTG
3834548 ATAATAT-TA-AAATATATACATA
1 ATAATATATATAAATATATACATA
* *
3834570 ATATTATATATAAAT-TATTCAT-
1 ATAATATATATAAATATATACATA
3834592 ATAATATATAT
1 ATAATATATAT
3834603 TAAAAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 8 0.29
24 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATATAAATATATACATA
Found at i:3834902 original size:3 final size:3
Alignment explanation
Indices: 3834886--3834941 Score: 78
Period size: 3 Copynumber: 18.3 Consensus size: 3
3834876 ACTAATGTAC
3834886 AAT AAT AACT -AT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
3834932 ATT AAT AAT A
1 AAT AAT AAT A
3834942 TGAAAATAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 43 0.90
4 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3835831 original size:35 final size:35
Alignment explanation
Indices: 3835785--3835853 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
3835775 GGGTGTGTGA
3835785 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
*
3835820 TGGTGCTGGTGGTAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3835854 AGAGGCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.10, G:0.51, T:0.19
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:3837891 original size:46 final size:46
Alignment explanation
Indices: 3837833--3838048 Score: 256
Period size: 46 Copynumber: 4.7 Consensus size: 46
3837823 GATATTTAGG
* *
3837833 CATCCGACCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
3837879 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * * * * *
3837925 CGTCCGAACTCGTTGAGTTGAGTCCTAGTTC-GTGAAATGTA-ACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-A
*
3837972 CATCCGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
3838018 CGCCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC
3838049 GGTTATGGGC
Statistics
Matches: 140, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
45 1 0.01
46 104 0.74
47 34 0.24
48 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:3837998 original size:93 final size:93
Alignment explanation
Indices: 3837879--3838049 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3837869 TGGATGCGAA
*
3837879 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
1 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
*
3837944 GAGTCCTAGTTCGTGAAATGTAACTAGG
66 GAGTCCGAGTTCGTGAAATGTAACTAGG
* * *
3837972 CATCCGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAACGCCCGAGCTCGTTGAGTT
1 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
3838037 GAGTCCGAGTTCG
66 GAGTCCGAGTTCG
3838050 GTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (93 bp):
CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAAATGTAACTAGG
Found at i:3847078 original size:24 final size:26
Alignment explanation
Indices: 3847040--3847096 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
3847030 ATTAAAAGAT
*
3847040 ATATATATATATAAAATGTATACATG
1 ATATATATATATAAAATATATACATG
*
3847066 ATATA-ATAT-TAAAATATTTACATG
1 ATATATATATATAAAATATATACATG
*
3847090 GTATATA
1 ATATATA
3847097 CATAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 17 0.63
25 5 0.19
26 5 0.19
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (26 bp):
ATATATATATATAAAATATATACATG
Found at i:3847095 original size:26 final size:27
Alignment explanation
Indices: 3847039--3847104 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 27
3847029 TATTAAAAGA
*
3847039 TATATATATATATAAAATGTATACATG
1 TATATATATATATAAAATATATACATG
*
3847066 -ATATA-ATAT-TAAAATATTTACATGG
1 TATATATATATATAAAATATATACAT-G
*
3847091 TATATACATA-ATAA
1 TATATATATATATAA
3847105 TGTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 12 0.36
25 5 0.15
26 10 0.30
27 6 0.18
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (27 bp):
TATATATATATATAAAATATATACATG
Found at i:3847692 original size:39 final size:38
Alignment explanation
Indices: 3847600--3847748 Score: 190
Period size: 39 Copynumber: 3.9 Consensus size: 38
3847590 TTCCACTCCC
* * * * *
3847600 CCCATGCTACTTTGTTTTATTATTAATCAAAACCACTC
1 CCCATACTATTTTGTTTTATTATTAATTAAAACTACTT
* *
3847638 CCCATGCTATTTTGTTTTATTGTTAATTAAAACTACTTT
1 CCCATACTATTTTGTTTTATTATTAATTAAAACTAC-TT
* *
3847677 CCCATACTATTTTGTTTTCTTGTTAATTAAAACTACTT
1 CCCATACTATTTTGTTTTATTATTAATTAAAACTACTT
*
3847715 CCTCATACCATTTTGTTTTATTATTAATTAAAAC
1 CC-CATACTATTTTGTTTTATTATTAATTAAAAC
3847749 CATACTTTAT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
38 36 0.36
39 63 0.64
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (38 bp):
CCCATACTATTTTGTTTTATTATTAATTAAAACTACTT
Found at i:3850160 original size:28 final size:28
Alignment explanation
Indices: 3850128--3850182 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3850118 TTTTGTATTC
3850128 ATTTATATGGTTAAATCACATGTAATAT
1 ATTTATATGGTTAAATCACATGTAATAT
3850156 ATTTATATGGTTAAATCACATGTAATA
1 ATTTATATGGTTAAATCACATGTAATA
3850183 GCAAACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (28 bp):
ATTTATATGGTTAAATCACATGTAATAT
Found at i:3852241 original size:15 final size:15
Alignment explanation
Indices: 3852221--3852250 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3852211 ATTTTTACTA
3852221 TTTTTTAGTTTTTAT
1 TTTTTTAGTTTTTAT
*
3852236 TTTTTTATTTTTTAT
1 TTTTTTAGTTTTTAT
3852251 GATCTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTAGTTTTTAT
Found at i:3869101 original size:20 final size:20
Alignment explanation
Indices: 3869076--3869113 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3869066 TAAAATAGTA
* *
3869076 ACAAAATTAACAATAAAACT
1 ACAAAATAAACAACAAAACT
3869096 ACAAAATAAACAACAAAA
1 ACAAAATAAACAACAAAA
3869114 TAGTAGCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (20 bp):
ACAAAATAAACAACAAAACT
Found at i:3869186 original size:21 final size:21
Alignment explanation
Indices: 3869162--3869202 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3869152 AAAATAATAA
3869162 CAAGAA-AATAGAAAAAAAAAG
1 CAAGAATAATA-AAAAAAAAAG
*
3869183 CAAGAATAGTAAAAAAAAAA
1 CAAGAATAATAAAAAAAAAA
3869203 CAGCAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
CAAGAATAATAAAAAAAAAAG
Found at i:3870485 original size:18 final size:19
Alignment explanation
Indices: 3870451--3870487 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
3870441 TTAAATTTAT
3870451 TAAATAAAATATACATTAA
1 TAAATAAAATATACATTAA
3870470 TAAA-AAAAT-TAGCATTAA
1 TAAATAAAATATA-CATTAA
3870488 CACAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAATAAAATATACATTAA
Found at i:3870674 original size:25 final size:25
Alignment explanation
Indices: 3870633--3870683 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
3870623 AGTAAATTTC
3870633 TTTTTTGGTCACTCAACAATTCGAAT
1 TTTTTTGGTCACTCAACAATT-GAAT
*
3870659 TTTTTTTGTCAC-CAACAATTGAAT
1 TTTTTTGGTCACTCAACAATTGAAT
3870683 T
1 T
3870684 ACTAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 8 0.33
26 11 0.46
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (25 bp):
TTTTTTGGTCACTCAACAATTGAAT
Found at i:3874124 original size:31 final size:32
Alignment explanation
Indices: 3874062--3874124 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
3874052 ACAAAATTTT
* *
3874062 AATAAGACCTTAATATAATCATATAAACATTA
1 AATAAGACCTTAAAATAATAATATAAACATTA
* * *
3874094 AATAA-ACTTTAAAATAATAATTTAATCATTA
1 AATAAGACCTTAAAATAATAATATAAACATTA
3874125 GAATTGTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (32 bp):
AATAAGACCTTAAAATAATAATATAAACATTA
Found at i:3877126 original size:21 final size:23
Alignment explanation
Indices: 3877086--3877127 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3877076 AAACAGTAGC
*
3877086 TATTCATTTATTTAGTTATTTCA
1 TATTCATTTATATAGTTATTTCA
3877109 TATT-ATTTATAT-GTTATTT
1 TATTCATTTATATAGTTATTT
3877128 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (23 bp):
TATTCATTTATATAGTTATTTCA
Found at i:3887471 original size:171 final size:171
Alignment explanation
Indices: 3887174--3887514 Score: 583
Period size: 171 Copynumber: 2.0 Consensus size: 171
3887164 CGCCAAAAAA
* *
3887174 TGTGAAAACTTCGTTAATTGATCAACTATTACCCAGATGGCATTTCTTTTGCAGGGTGAAGTCGG
1 TGTGAAAACTTCGTTAATTGATCAACTATTACCCAGATGGCATTTATTTTGCAGGGTGAAGTCAG
* *
3887239 CATGCCAACTACAAAATCCATCGTAATATGTTCCCATTTTTATTCTAGAATAAAAATTGGTTGTA
66 CATGCCAACTACAAAACCCATCGTAATATGTTCCCATTTTCATTCTAGAATAAAAATTGGTTGTA
3887304 ATAAACCAATAGGAACTTGATGCTAGGCATTTACTCGCTAT
131 ATAAACCAATAGGAACTTGATGCTAGGCATTTACTCGCTAT
* * *
3887345 TGTGCAAACTTTGTTAATTGATCAACTATTACCCAGATGGCATTTATTTTGCTGGGTGAAGTCAG
1 TGTGAAAACTTCGTTAATTGATCAACTATTACCCAGATGGCATTTATTTTGCAGGGTGAAGTCAG
* *
3887410 CATGCCAACTACAAAACCCATCGTGATATGTTCCCATTTTCATTCTGGAATAAAAATTGGTTGTA
66 CATGCCAACTACAAAACCCATCGTAATATGTTCCCATTTTCATTCTAGAATAAAAATTGGTTGTA
* *
3887475 ATAAACCAATAGGAACTTGATGCTCGGCCTTTACTCGCTA
131 ATAAACCAATAGGAACTTGATGCTAGGCATTTACTCGCTA
3887515 AAAGGTTAGA
Statistics
Matches: 159, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
171 159 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (171 bp):
TGTGAAAACTTCGTTAATTGATCAACTATTACCCAGATGGCATTTATTTTGCAGGGTGAAGTCAG
CATGCCAACTACAAAACCCATCGTAATATGTTCCCATTTTCATTCTAGAATAAAAATTGGTTGTA
ATAAACCAATAGGAACTTGATGCTAGGCATTTACTCGCTAT
Found at i:3889719 original size:4 final size:4
Alignment explanation
Indices: 3889710--3889750 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
3889700 GGTTTATAGT
* *
3889710 GAAA GAAA GAAA GAAA -AAA AAAA GAAA GAAA -AAA AAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
3889751 GATAATAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.18
4 27 0.82
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3889735 original size:15 final size:15
Alignment explanation
Indices: 3889715--3889750 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3889705 ATAGTGAAAG
3889715 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
3889730 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
3889745 AAAGAA
1 AAAGAA
3889751 GATAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:3889735 original size:19 final size:18
Alignment explanation
Indices: 3889711--3889752 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3889701 GTTTATAGTG
3889711 AAAGAAAGAAAGAAAAAAA
1 AAAGAAAGAAA-AAAAAAA
3889730 AAAGAAAGAAAAAAAAAA
1 AAAGAAAGAAAAAAAAAA
*
3889748 GAAGA
1 AAAGA
3889753 TAATAAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAAAAAAAA
Found at i:3892524 original size:19 final size:21
Alignment explanation
Indices: 3892470--3892524 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 21
3892460 CATAAGTCTA
*
3892470 AAAAAAATTTAAATATATGTAT
1 AAAAAAATAT-AATATATGTAT
*
3892492 AAAACACATA-AATAT-T-TAT
1 AAAA-AAATATAATATATGTAT
3892511 AAAAAAATATAATA
1 AAAAAAATATAATA
3892525 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 1 0.04
21 5 0.18
22 4 0.14
23 3 0.11
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAAAATATAATATATGTAT
Found at i:3892549 original size:6 final size:6
Alignment explanation
Indices: 3892540--3892564 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3892530 TTTAAATTTT
3892540 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
3892565 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:3896799 original size:11 final size:11
Alignment explanation
Indices: 3896785--3896825 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3896775 TGTTTTCTCC
3896785 CTATTTTGCTA
1 CTATTTTGCTA
*
3896796 CTATTTTACTA
1 CTATTTTGCTA
* *
3896807 TTATGTTGCTA
1 CTATTTTGCTA
3896818 CTATTTTG
1 CTATTTTG
3896826 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:3896973 original size:12 final size:12
Alignment explanation
Indices: 3896943--3896974 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3896933 TATATATTTT
3896943 AAAATT-ATATA
1 AAAATTAATATA
3896954 AAAA-TAATATA
1 AAAATTAATATA
3896965 AAAATTAATA
1 AAAATTAATA
3896975 CGGGCGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 13 0.68
12 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:3897474 original size:21 final size:21
Alignment explanation
Indices: 3897448--3897502 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3897438 CTTTTACGAC
3897448 CTTCTGTTCAGCTCTTATGAG
1 CTTCTGTTCAGCTCTTATGAG
*
3897469 CTTCTGTTAAGCTCTTATGAG
1 CTTCTGTTCAGCTCTTATGAG
3897490 CTTCTGTTCAGCT
1 CTTCTGTTCAGCT
3897503 TTCAAGCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
CTTCTGTTCAGCTCTTATGAG
Found at i:3905190 original size:15 final size:15
Alignment explanation
Indices: 3905166--3905195 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3905156 TAATTCATGC
*
3905166 ATTTTGTTTAAATTT
1 ATTTTCTTTAAATTT
3905181 ATTTTCTTTAAATTT
1 ATTTTCTTTAAATTT
3905196 TTATATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
ATTTTCTTTAAATTT
Found at i:3909675 original size:10 final size:10
Alignment explanation
Indices: 3909655--3909699 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
3909645 TTTAAAAACC
3909655 ATTAAAA-TT
1 ATTAAAATTT
3909664 ATTAAAATTT
1 ATTAAAATTT
3909674 ATTAAAATTT
1 ATTAAAATTT
* *
3909684 TTTAATATTT
1 ATTAAAATTT
3909694 -TTAAAA
1 ATTAAAA
3909700 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
9 12 0.38
10 20 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTAAAATTT
Found at i:3909705 original size:19 final size:20
Alignment explanation
Indices: 3909658--3909710 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3909648 AAAAACCATT
3909658 AAAATTATTAAAATTTATTAA
1 AAAATT-TTAAAATTTATTAA
** *
3909679 AATTTTTTAATATTT-TTAA
1 AAAATTTTAAAATTTATTAA
3909698 AAAATTTTAAAAT
1 AAAATTTTAAAAT
3909711 AATTAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 14 0.54
20 8 0.31
21 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTTTAAAATTTATTAA
Found at i:3909709 original size:9 final size:9
Alignment explanation
Indices: 3909656--3909710 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 9
3909646 TTAAAAACCA
*
3909656 TTAAAATTA
1 TTAAAATTT
3909665 TTAAAATTT
1 TTAAAATTT
3909674 ATTAAAATTTT
1 -TTAAAA-TTT
*
3909685 TTAATATTT
1 TTAAAATTT
*
3909694 TTAAAAAATT
1 TT-AAAATTT
3909704 TTAAAAT
1 TTAAAAT
3909711 AATTAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.45
10 18 0.47
11 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTAAAATTT
Found at i:3912898 original size:26 final size:26
Alignment explanation
Indices: 3912789--3912890 Score: 186
Period size: 26 Copynumber: 3.9 Consensus size: 26
3912779 CATGAAATTC
3912789 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3912815 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3912841 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3912867 TTATCATGAAACATTTACCTAACC
1 TTATCATGAAACATTTACCTAACC
3912891 TTTTATCAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3917141 original size:16 final size:16
Alignment explanation
Indices: 3917116--3917154 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3917106 CATTCTTTAT
*
3917116 AAAATTTTTGTTTTTG
1 AAAATCTTTGTTTTTG
3917132 AAAATCTTTGTTTTTG
1 AAAATCTTTGTTTTTG
*
3917148 TAAATCT
1 AAAATCT
3917155 ATCCCACAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (16 bp):
AAAATCTTTGTTTTTG
Found at i:3919958 original size:26 final size:26
Alignment explanation
Indices: 3919848--3919949 Score: 168
Period size: 26 Copynumber: 3.9 Consensus size: 26
3919838 CATGAAATTC
3919848 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3919874 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3919900 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
3919926 TTATCAAGGAACATTTACCTAACC
1 TTATCATGAAACATTTACCTAACC
3919950 TTTTATCAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3923849 original size:28 final size:28
Alignment explanation
Indices: 3923794--3923849 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3923784 AACCTGAAAT
**
3923794 ATAGACCTAAAATTTTACCCAAGTCATG
1 ATAGACCTAAAATTTTACCCAAACCATG
*
3923822 ATAGACCTAAAATTTTGCCCAAACCATG
1 ATAGACCTAAAATTTTACCCAAACCATG
3923850 TCATATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (28 bp):
ATAGACCTAAAATTTTACCCAAACCATG
Found at i:3926724 original size:20 final size:20
Alignment explanation
Indices: 3926691--3926729 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3926681 ATGATAATAA
* *
3926691 ATAAAACAATAAAAGAAATG
1 ATAAAAAAAGAAAAGAAATG
*
3926711 ATAAAAAAAGAAAATAAAT
1 ATAAAAAAAGAAAAGAAAT
3926730 AAGTGAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (20 bp):
ATAAAAAAAGAAAAGAAATG
Found at i:3928487 original size:44 final size:44
Alignment explanation
Indices: 3928405--3928882 Score: 210
Period size: 44 Copynumber: 10.6 Consensus size: 44
3928395 CTTTAACCCG
* * ** * *
3928405 CTCCATTGCAACTTCAGGGAGATAGGATTAGAAGCTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAATCTA
* *
3928449 TTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAATCTA
* * * * *
3928493 CCCCACTACAACCTT-AGGGAGATAAGA-CTTGTAAT-TTCAACCTG
1 CTCCACTGCAA-CTTCAGGGAGATAAGATC-GGT-ATCTTCAATCTA
** * * * * * * * *
3928537 CTTTATTGCAACTTTAGAGAGATAAGGTTTGCTATCTTCAATATG
1 CTCCACTGCAACTTCAGGGAGATAA-GATCGGTATCTTCAATCTA
* * * ** *
3928582 CTCCACTGCAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTGATTTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-TCG------GTATCTTCAATCTA
* ** * * * *
3928633 TTCCACTGCAACTTCAGAAAAATAAGATTCGCTGTCTTTAGA-CTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-TCGGTATCTTCA-ATCTA
* * * *
3928678 CTCCACTGCAACTTTAGGGAAATAAGACTC-GTAACTTCAACCTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-TCGGTATCTTCAATCTA
* * * *** * * *
3928722 CTCTACTGCAACTTCAGAGAGATAAGGTTTATAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAATCTA
* * * * * *
3928766 CTCTACTGCAACTTCAGAGAGATAATATTTGCTATCTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-TCGGTATCTTCAATCTA
* * * ** * *
3928811 CTCCACTACAACTTTAGGGAGATAAGATCTGTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAATCTA
* *
3928855 CTCCACTACAACTTTAGGGAGATAAGAT
1 CTCCACTGCAACTTCAGGGAGATAAGAT
3928883 TTGTAATTTG
Statistics
Matches: 330, Mismatches: 86, Indels: 36
0.73 0.19 0.08
Matches are distributed among these distances:
43 6 0.02
44 185 0.56
45 105 0.32
46 1 0.00
51 33 0.10
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAATCTA
Found at i:3928734 original size:185 final size:183
Alignment explanation
Indices: 3928447--3928796 Score: 457
Period size: 185 Copynumber: 1.9 Consensus size: 183
3928437 AGCTTCAATC
** * * *
3928447 TATTCCACTGCAACTTCAGGGAGATAAGATCGGTATCTTCAGTCTACCCCACTACAACCTTAGGG
1 TATTCCACTGCAACTTCAGAAAAATAAGATCGCTATCTTCAGACTACCCCACTACAACCTTAGGG
* * * * * * * * *
3928512 AGATAAGACTTGTAATTTCAACCTGCTTTATTGCAACTTTAGAGAGATAAGGTTTGCTATCTTCA
66 AAATAAGACTCGTAACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTT-ATAGCTTCA
* *
3928577 ATATGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTGATT
130 ATATGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTGATT
* * * * *
3928631 TATTCCACTGCAACTTCAGAAAAATAAGATTCGCTGTCTTTAGACTACTCCACTGCAACTTTAGG
1 TATTCCACTGCAACTTCAGAAAAATAAGA-TCGCTATCTTCAGACTACCCCACTACAACCTTAGG
*
3928696 GAAATAAGACTCGTAACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTTATAGCTTTA
65 GAAATAAGACTCGTAACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTTATAGCTTCA
* * *
3928761 ATCTGCTCTACTGCAACTTCAGAGAGATAATATTTG
130 ATATGCTCCACTGCAACTTCAGAGAGATAAGATTTG
3928797 CTATCTTTAA
Statistics
Matches: 140, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
184 63 0.45
185 77 0.55
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (183 bp):
TATTCCACTGCAACTTCAGAAAAATAAGATCGCTATCTTCAGACTACCCCACTACAACCTTAGGG
AAATAAGACTCGTAACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTTATAGCTTCAA
TATGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTGATT
Found at i:3928804 original size:133 final size:133
Alignment explanation
Indices: 3928634--3929064 Score: 402
Period size: 133 Copynumber: 3.2 Consensus size: 133
3928624 TTTGATTTAT
* * *
3928634 TCCACTGCAACTTCAGAAAAATAAGATTCGCTGTCTTTAGACTACTCCACTGCAACTTTAGGGAA
1 TCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTTAGACTACTCCACTGCAACTTTAGGGAG
* *
3928699 ATAAGACTCGTAACTTCAACCTACTCTACTGCAACTTCAGAGAGATAAGGTTTATAGCTTTAATC
66 ATAAGACTCGTAACTTCAACCTGCTCTACTACAACTTCAGAGAGATAAGGTTTATAGCTTTAATC
3928764 TGC
131 TGC
* * * * *
3928767 TCTACTGCAACTTCA-GAGAGATAATATTTGCTATCTTTA-ATCTACTCCACTACAACTTTAGGG
1 TCCACTGCAACTTCAGGA-AAATAAGATTCGCTATCTTTAGA-CTACTCCACTGCAACTTTAGGG
** * * * * * *
3928830 AGATAAGA-TCTGTGGCTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGTAATTTGT
64 AGATAAGACTC-GTAACTTCAACCTGCTCTACTACAACTTCAGAGAGATAAG----G---TTTAT
*
3928894 AGCTTTAATCTGT
121 AGCTTTAATCTGC
* * * * * *
3928907 TCCATTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACTTTAGTGAG
1 TCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTTAGACTACTCCACTGCAACTTTAGGGAG
* * * * * * * * *
3928972 ATAAGACTTGTCATTTCAACTTGCT-TCACTTCAACTTCAGAGAGATAAGATTTATGGTTTTAGT
66 ATAAGACTCGTAACTTCAACCTGCTCT-ACTACAACTTCAGAGAGATAAGGTTTATAGCTTTAAT
*
3929036 TTGC
130 CTGC
* *
3929040 TCCACTGCATCTTCAGGAAGATAAG
1 TCCACTGCAACTTCAGGAAAATAAG
3929065 GTTTATGGCT
Statistics
Matches: 233, Mismatches: 51, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
132 4 0.02
133 124 0.53
137 1 0.00
140 101 0.43
141 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (133 bp):
TCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTTAGACTACTCCACTGCAACTTTAGGGAG
ATAAGACTCGTAACTTCAACCTGCTCTACTACAACTTCAGAGAGATAAGGTTTATAGCTTTAATC
TGC
Found at i:3928955 original size:140 final size:138
Alignment explanation
Indices: 3928580--3929024 Score: 458
Period size: 140 Copynumber: 3.2 Consensus size: 138
3928570 ATCTTCAATA
* * * * *
3928580 TGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTGATTTATTCCACTGCAAC
1 TGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTGCAAC
* * * *
3928645 TTCAGAAAAATAAGATTCGCTGTCTTTAGACTACTCCACTGCAACTTTAGGGAAATAAGACTCGT
66 TTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTCCACTGCAACTTTAGGGAGATAAGACT-GT
* *
3928710 AACTTCAACC
130 GACTTTAA-C
* * * * *
3928720 TACTCTACTGCAACTTCAGAGAGATAAG----G---TTTATAGCTTTAATCTGCTCTACTGCAAC
1 TGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTGCAAC
* * * * *
3928778 TTCA-GAGAGATAATATTTGCTATCTTTAATCTACTCCACTACAACTTTAGGGAGATAAGATCTG
66 TTCAGGA-AAATAAGATTCGCTATCTTTAGTCTACTCCACTGCAACTTTAGGGAGATAAGA-CTG
*
3928842 TGGCTTTAATC
129 TGACTTTAA-C
* * * *
3928853 TGCTCCACTACAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCATTGCAAC
1 TGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTGCAAC
* * * *
3928918 TTCAGGAAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACTTTAGTGAGATAAGACT-TG
66 TTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTGTG
*
3928982 TCATTTCAAC
131 AC-TTT-AAC
* *
3928992 TTGCTTCACTTCAACTTCAGAGAGATAAGATTT
1 -TGCTCCACTGCAACTTCAGAGAGATAAGATTT
3929025 ATGGTTTTAG
Statistics
Matches: 246, Mismatches: 46, Indels: 26
0.77 0.14 0.08
Matches are distributed among these distances:
132 1 0.00
133 103 0.42
134 2 0.01
136 1 0.00
137 1 0.00
138 3 0.01
139 6 0.02
140 127 0.52
141 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (138 bp):
TGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTGCAAC
TTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTGTG
ACTTTAAC
Found at i:3929040 original size:44 final size:43
Alignment explanation
Indices: 3928726--3929112 Score: 206
Period size: 44 Copynumber: 8.6 Consensus size: 43
3928716 AACCTACTCT
* * * * *
3928726 ACTGCAACTTCAGAGAGATAAGGTTTATAGCTTTAATCTGCTCT
1 ACTGCAACTTCAG-GAGATAAGATTTATGGCTTTAGTTTGCTCC
* * ** * * *
3928770 ACTGCAACTTCAGAGAGATAATATTTGCTATCTTTAATCTACTCC
1 ACTGCAACTTCAG-GAGATAAGATTT-ATGGCTTTAGTTTGCTCC
* * * * * *
3928815 ACTACAACTTTAGGGAGATAAGATCTGTGGCTTTAATCTGCTCC
1 ACTGCAACTTCA-GGAGATAAGATTTATGGCTTTAGTTTGCTCC
* * * * *
3928859 ACTACAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCC
1 ACTGCAACTTCA-GGAGATAAGA-TT-T-A--TG--GCTTTAGTTTGCTCC
* * * *
3928910 ATTGCAACTTCAGGAAAATAAGATTCGCTAT--CTTCAGTCTGCTCC
1 ACTGCAACTTCAGG-AGATAAGATT---TATGGCTTTAGTTTGCTCC
* * * * ** *
3928955 ACTGTAACTTTAGTGAGATAAGA-CT-TGTCATTTCAACTTGCTTC
1 ACTGCAACTTCAG-GAGATAAGATTTATGGC-TTT-AGTTTGCTCC
* *
3928999 ACTTCAACTTCAGAGAGATAAGATTTATGGTTTTAGTTTGCTCC
1 ACTGCAACTTCAG-GAGATAAGATTTATGGCTTTAGTTTGCTCC
* *
3929043 ACTGCATCTTCAGGAAGATAAGGTTTATGGCTTTAGTTTGCTCC
1 ACTGCAACTTCAGG-AGATAAGATTTATGGCTTTAGTTTGCTCC
3929087 ACTGCAACTTCCAGGAGATAAGATTT
1 ACTGCAACTT-CAGGAGATAAGATTT
3929113 GTCATGGTAG
Statistics
Matches: 271, Mismatches: 51, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 1 0.00
43 3 0.01
44 150 0.55
45 71 0.26
46 5 0.02
49 3 0.01
50 4 0.01
51 31 0.11
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (43 bp):
ACTGCAACTTCAGGAGATAAGATTTATGGCTTTAGTTTGCTCC
Found at i:3929268 original size:44 final size:44
Alignment explanation
Indices: 3929188--3929276 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
3929178 AATCCATTAT
** * *
3929188 ACTGCAACTTCGGTGAAATAAGATTCGTATTCTCAATCTGCTCC
1 ACTGCAACTTCAATGAAATAAGATTAGTATTCTCAATCTACTCC
* *
3929232 ACTGCAACTTCAATGAGATAAGATTAGTGGTT-TCAATCTACTCC
1 ACTGCAACTTCAATGAAATAAGATTAGT-ATTCTCAATCTACTCC
3929276 A
1 A
3929277 TTGTAATTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 36 0.95
45 2 0.05
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (44 bp):
ACTGCAACTTCAATGAAATAAGATTAGTATTCTCAATCTACTCC
Found at i:3941186 original size:20 final size:20
Alignment explanation
Indices: 3941163--3941210 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3941153 TTAAAATATG
* * *
3941163 ATAATTAATAAAACAATAAA
1 ATAAATAATAAAAAAAGAAA
*
3941183 ATAAATGATAAAAAAAGAAA
1 ATAAATAATAAAAAAAGAAA
3941203 ATAAATAA
1 ATAAATAA
3941211 GTGAAAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (20 bp):
ATAAATAATAAAAAAAGAAA
Found at i:3943621 original size:22 final size:22
Alignment explanation
Indices: 3943591--3943641 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3943581 TTTTATTCGT
3943591 AAAAAAATTTGAAAAAAAAAAG
1 AAAAAAATTTGAAAAAAAAAAG
* *
3943613 AGAAAAATTTGAAAAACAAAAG
1 AAAAAAATTTGAAAAAAAAAAG
3943635 AAAAAAA
1 AAAAAAA
3943642 AAGAACAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAAAAATTTGAAAAAAAAAAG
Found at i:3943660 original size:32 final size:31
Alignment explanation
Indices: 3943603--3943664 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
3943593 AAAAATTTGA
*
3943603 AAAAAAAAAGAGAAAAATTTGAAAAACAAAAG
1 AAAAAAAAAGAGAAAAATTTCAAAAA-AAAAG
*
3943635 AAAAAAAAAGA-ACAAGATTTCAAAAAAAAA
1 AAAAAAAAAGAGA-AAAATTTCAAAAAAAAA
3943665 TTGAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (31 bp):
AAAAAAAAAGAGAAAAATTTCAAAAAAAAAG
Found at i:3944936 original size:13 final size:12
Alignment explanation
Indices: 3944918--3944952 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3944908 GTTTTTCTCT
3944918 CTTTTTTTTATC
1 CTTTTTTTTATC
*
3944930 TTATTTTTTTATC
1 CT-TTTTTTTATC
3944943 CTTTTTTTTA
1 CTTTTTTTTA
3944953 GAAAAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTTTTTTTATC
Found at i:3945640 original size:26 final size:26
Alignment explanation
Indices: 3945610--3946059 Score: 152
Period size: 26 Copynumber: 17.4 Consensus size: 26
3945600 AAACATATAT
3945610 TTTATTTTAAATAGTTTTATATATTA
1 TTTATTTTAAATAGTTTTATATATTA
* ** *
3945636 TTTATTTTATATTTTTTTACATATTA
1 TTTATTTTAAATAGTTTTATATATTA
* * * * * *
3945662 GTTCTCTTAAACTA-TTTAATTTATCA
1 TTTATTTTAAA-TAGTTTTATATATTA
* * * **
3945688 TTTATTTAAAATTG-ATT-TATGGTA
1 TTTATTTTAAATAGTTTTATATATTA
* * * *
3945712 TTCATTTCAAATTGTTTTAT-T-GTA
1 TTTATTTTAAATAGTTTTATATATTA
3945736 TATTATTTT--A-AGTTATATATATATTAA
1 T-TTATTTTAAATAGTT-T-TATATATT-A
* ** *
3945763 CTAGTTACTTTAAACGGTTTTAT-TA-CA
1 -T--TTATTTTAAATAGTTTTATATATTA
3945790 TATTATTTTAAATTA-TTTTATATATTA
1 T-TTATTTTAAA-TAGTTTTATATATTA
**
3945817 TTTATTTTACGT--TTTTATATATACTA
1 TTTATTTTAAATAGTTTTATATAT--TA
*
3945843 TTTATTTTAAA-A-TTTTACATATTA
1 TTTATTTTAAATAGTTTTATATATTA
*
3945867 TATATTTTAAAT--TTTTATATATGTTA
1 TTTATTTTAAATAGTTTTATATA--TTA
* * * *
3945893 TGTAGTTCAAACTA-TTTTATATGTTA
1 TTTATTTTAAA-TAGTTTTATATATTA
** *
3945919 TTTATTTTAAAATTCTTTTATATATTG
1 TTTATTTT-AAATAGTTTTATATATTA
*
3945946 TTTATTTCAAACT-GTTTTAT-TATTA
1 TTTATTTTAAA-TAGTTTTATATATTA
* * **
3945971 TTTACTTTAATTTTTTTATATATATTA
1 TTTATTTTAAATAGTTT-TATATATTA
* * * *
3945998 TTTATTTGAGAT-TTTTTTTAT-TTA
1 TTTATTTTAAATAGTTTTATATATTA
* * * *
3946022 TTCATTTTGAATTGTTCTTATACATTA
1 TTTATTTTAAATAGTT-TTATATATTA
3946049 TTTATTTTAAA
1 TTTATTTTAAA
3946060 CCATTATTTA
Statistics
Matches: 311, Mismatches: 78, Indels: 69
0.68 0.17 0.15
Matches are distributed among these distances:
22 3 0.01
23 2 0.01
24 64 0.21
25 48 0.15
26 117 0.38
27 52 0.17
28 9 0.03
29 8 0.03
30 3 0.01
31 2 0.01
32 3 0.01
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (26 bp):
TTTATTTTAAATAGTTTTATATATTA
Found at i:3945723 original size:24 final size:24
Alignment explanation
Indices: 3945691--3945736 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3945681 TTTATCATTT
3945691 ATTTAAAATTGATTTATGGTATTC
1 ATTTAAAATTGATTTATGGTATTC
* * *
3945715 ATTTCAAATTGTTTTATTGTAT
1 ATTTAAAATTGATTTATGGTAT
3945737 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (24 bp):
ATTTAAAATTGATTTATGGTATTC
Found at i:3945837 original size:24 final size:24
Alignment explanation
Indices: 3945792--3946059 Score: 171
Period size: 26 Copynumber: 10.4 Consensus size: 24
3945782 TTATTACATA
3945792 TTATTTTAAATTATTTTATATATTAT
1 TTATTTTAAA-T-TTTTATATATTAT
**
3945818 TTATTTTACGTTTTTATATATACTAT
1 TTATTTTAAATTTTTATATAT--TAT
* *
3945844 TTATTTTAAAATTTTACATATTAT
1 TTATTTTAAATTTTTATATATTAT
*
3945868 ATATTTTAAATTTTTATATATGTTAT
1 TTATTTTAAATTTTTATATA--TTAT
* * * *
3945894 GTAGTTCAAACTATTTTATATGTTAT
1 TTATTTTAAA-T-TTTTATATATTAT
*
3945920 TTATTTTAAAATTCTTTTATATATTGT
1 TTATTTT-AAA-T-TTTTATATATTAT
*
3945947 TTATTTCAAACTGTTTTAT-TATTAT
1 TTATTTTAAA-T-TTTTATATATTAT
* *
3945972 TTACTTTAATTTTTTTATATATATTAT
1 TTATTTTAA--ATTTT-TATATATTAT
* * *
3945999 TTATTTGAGATTTTT-TTTATTTAT
1 TTATTTTAAATTTTTATATA-TTAT
* * *
3946023 TCATTTTGAATTGTTCTTATACATTAT
1 TTATTTT-AAAT-TT-TTATATATTAT
3946050 TTATTTTAAA
1 TTATTTTAAA
3946060 CCATTATTTA
Statistics
Matches: 186, Mismatches: 40, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
23 3 0.02
24 40 0.22
25 22 0.12
26 65 0.35
27 46 0.25
28 10 0.05
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
TTATTTTAAATTTTTATATATTAT
Found at i:3945925 original size:52 final size:52
Alignment explanation
Indices: 3945792--3946060 Score: 228
Period size: 52 Copynumber: 5.2 Consensus size: 52
3945782 TTATTACATA
* * ** *
3945792 TTATTTTAAATTATTTTATATATTATTTATTTTACGTTTTTATATATACTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAAATTTTTATATATATTAT
* * * *
3945844 TTATTTTAAA--ATTTTACATATTATATATTTTAAATTTTTATATATGTTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAAATTTTTATATATATTAT
* * * *
3945894 GTAGTTCAAACTATTTTATATGTTATTTATTTTAAAATTCTTT-TATATATTGT
1 TTATTTCAAACTATTTTATATATTATTTATTTT-AAATT-TTTATATATATTAT
* * *
3945947 TTATTTCAAACTGTTTTAT-TATTATTTACTTTAATTTTTTTATATATATTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAA-ATTTTTATATATATTAT
* * * * * * *
3945999 TTATTTGAGA-TTTTTTTTAT-TTATTCATTTTGAATTGTTCT-TATACATTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAAATT-TT-TATATATATTAT
*
3946050 TTATTTTAAAC
1 TTATTTCAAAC
3946061 CATTATTTAC
Statistics
Matches: 175, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
50 43 0.25
51 40 0.23
52 60 0.34
53 29 0.17
54 3 0.02
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (52 bp):
TTATTTCAAACTATTTTATATATTATTTATTTTAAATTTTTATATATATTAT
Found at i:3947857 original size:20 final size:20
Alignment explanation
Indices: 3947824--3947895 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
3947814 TTATGGAGTG
* *
3947824 AAAAACTATTAAAAAAATTT
1 AAAAATTATAAAAAAAATTT
*
3947844 AAAAATTAT-AAAAATATATT
1 AAAAATTATAAAAAAAAT-TT
* * * *
3947864 AATAATTCTAAAAATAGATAT
1 AAAAATTATAAAAA-AAATTT
3947885 AAAAATTATAA
1 AAAAATTATAA
3947896 GAACTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 7 0.17
20 17 0.41
21 14 0.34
22 3 0.07
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (20 bp):
AAAAATTATAAAAAAAATTT
Found at i:3947858 original size:9 final size:9
Alignment explanation
Indices: 3947831--3947905 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
3947821 GTGAAAAACT
*
3947831 ATTAAAAAA
1 ATTATAAAA
3947840 ATT-TAAAA
1 ATTATAAAA
3947848 ATTATAAAA
1 ATTATAAAA
*
3947857 ATATATTAATA
1 AT-TA-TAAAA
*
3947868 ATTCTAAAA
1 ATTATAAAA
3947877 ATAGATATAAAA
1 AT---TATAAAA
*
3947889 ATTATAAGA
1 ATTATAAAA
*
3947898 ACTATAAA
1 ATTATAAA
3947906 CCCTGTTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.13
9 28 0.54
10 3 0.06
11 6 0.12
12 8 0.15
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
ATTATAAAA
Found at i:3948007 original size:10 final size:10
Alignment explanation
Indices: 3947992--3948020 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
3947982 AAACTATTTA
3947992 ATTTTTTTTT
1 ATTTTTTTTT
3948002 A-TTTTTTTT
1 ATTTTTTTTT
3948011 ATTTTTTTTT
1 ATTTTTTTTT
3948021 CATATTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
ATTTTTTTTT
Done.