Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 6 of 187
Found at i:1339832 original size:14 final size:13
Alignment explanation
Indices: 1339791--1339833 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
1339781 TCATCCTTAA
1339791 TCTTTTTTTCT-T
1 TCTTTTTTTCTAT
*
1339803 TCTTTTTTTTTCAT
1 TCTTTTTTTCT-AT
1339817 TCATTTTTTTCTAT
1 TC-TTTTTTTCTAT
1339831 TCT
1 TCT
1339834 CTTTCTCGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.38
13 1 0.04
14 7 0.27
15 8 0.31
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTTTTCTAT
Found at i:1348590 original size:27 final size:28
Alignment explanation
Indices: 1348538--1348612 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
1348528 AAAAATTAAA
1348538 AAATATTAAAAGAATATATAAATGAT-T
1 AAATATTAAAAGAATATATAAATGATAT
*
1348565 AAATATTAAAA-ACTATGA-AAATTGATAT
1 AAATATTAAAAGAATAT-ATAAA-TGATAT
*
1348593 AAATATT-ATA-AATATATAAA
1 AAATATTAAAAGAATATATAAA
1348613 ATAATCTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 8 0.20
27 25 0.61
28 8 0.20
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATATTAAAAGAATATATAAATGATAT
Found at i:1348692 original size:9 final size:9
Alignment explanation
Indices: 1348571--1348732 Score: 67
Period size: 9 Copynumber: 16.7 Consensus size: 9
1348561 GATTAAATAT
*
1348571 TAAAAACTA
1 TAAAAATTA
*
1348580 TGAAAATTGA
1 TAAAAATT-A
1348590 TATAAATATTA
1 TA-AAA-ATTA
*
1348601 TAAATA-TA
1 TAAAAATTA
* *
1348609 TAAAATAATC
1 TAAAA-ATTA
1348619 TAATAAATTA
1 TAA-AAATTA
1348629 T-AAAATTAA
1 TAAAAATT-A
*
1348638 TAAAACATATT
1 TAAAA-AT-TA
*
1348649 TAAAATTTTA
1 TAAAA-ATTA
**
1348659 TAACAACGTA
1 TAA-AAATTA
*
1348669 TTAAAATTCTA
1 -TAAAAAT-TA
1348680 TAAAAATTA
1 TAAAAATTA
*
1348689 TAAAAAGTA
1 TAAAAATTA
*
1348698 TTAAAATTAA
1 TAAAAATT-A
*
1348708 TATAAACTTA
1 TA-AAAATTA
1348718 TAAAAATTA
1 TAAAAATTA
1348727 TAAAAA
1 TAAAAA
1348733 CTTGAATTGG
Statistics
Matches: 115, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
8 11 0.10
9 39 0.34
10 33 0.29
11 28 0.24
12 4 0.03
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1348705 original size:29 final size:29
Alignment explanation
Indices: 1348571--1348732 Score: 84
Period size: 29 Copynumber: 5.5 Consensus size: 29
1348561 GATTAAATAT
* * *
1348571 TAAAAACTATGAAAATTGATATAAATATTA
1 TAAAAAGTATTAAAATTAATATAAA-ATTA
* *
1348601 TAAATA-TA-TAAAA-TAATCTAATAAATTA
1 TAAAAAGTATTAAAATTAATAT-A-AAATTA
* * * *
1348629 T-AAAATTAATAAAA-CATATTTAAAATTTTA
1 TAAAAAGTATTAAAATTA-ATATAAAA--TTA
* *
1348659 TAACAACGTATTAAAATT-CTATAAAAATTA
1 TAA-AAAGTATTAAAATTAATAT-AAAATTA
*
1348689 TAAAAAGTATTAAAATTAATATAAACTTA
1 TAAAAAGTATTAAAATTAATATAAAATTA
* *
1348718 TAAAAATTATAAAAA
1 TAAAAAGTATTAAAA
1348733 CTTGAATTGG
Statistics
Matches: 102, Mismatches: 18, Indels: 25
0.70 0.12 0.17
Matches are distributed among these distances:
27 7 0.07
28 15 0.15
29 43 0.42
30 21 0.21
31 3 0.03
32 13 0.13
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (29 bp):
TAAAAAGTATTAAAATTAATATAAAATTA
Found at i:1348733 original size:19 final size:19
Alignment explanation
Indices: 1348678--1348735 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1348668 ATTAAAATTC
*
1348678 TATAAAAATTATAAAAA-G
1 TATAAAAATTATAAAAACT
* *
1348696 TATTAAAATTAATATAAACT
1 TATAAAAATT-ATAAAAACT
1348716 TATAAAAATTATAAAAACT
1 TATAAAAATTATAAAAACT
1348735 T
1 T
1348736 GAATTGGACC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 9 0.27
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
TATAAAAATTATAAAAACT
Found at i:1358135 original size:46 final size:46
Alignment explanation
Indices: 1358082--1358174 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
1358072 TACATAGGCT
* *
1358082 CTTCCACTCGTACCAATGTATCCCTTTCCCTATTTTGGAGTTTCTC
1 CTTCCACTCGCACCAATGTATCCCTTTCCCCATTTTGGAGTTTCTC
* *
1358128 CTTCCACTCGCACCAATGTATTCCTTTCCCCGTTTTGGAGTTTCTC
1 CTTCCACTCGCACCAATGTATCCCTTTCCCCATTTTGGAGTTTCTC
1358174 C
1 C
1358175 ACAAAAACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.14, C:0.34, G:0.12, T:0.40
Consensus pattern (46 bp):
CTTCCACTCGCACCAATGTATCCCTTTCCCCATTTTGGAGTTTCTC
Found at i:1361783 original size:17 final size:19
Alignment explanation
Indices: 1361749--1361795 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1361739 TATGCATGGT
*
1361749 AAATAATAAAAGTCAACAA
1 AAATAATAAAAGTAAACAA
1361768 AAATAA-AAAA-TAAACAA
1 AAATAATAAAAGTAAACAA
*
1361785 ACAAGAATAAA
1 A-AATAATAAA
1361796 GACATTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (19 bp):
AAATAATAAAAGTAAACAA
Found at i:1362269 original size:14 final size:15
Alignment explanation
Indices: 1362250--1362279 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1362240 TATATATATG
1362250 AATAATAAT-AATAA
1 AATAATAATAAATAA
1362264 AATAATAATAAATAA
1 AATAATAATAAATAA
1362279 A
1 A
1362280 TAAATGAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAATAAATAA
Found at i:1364064 original size:44 final size:42
Alignment explanation
Indices: 1364015--1364387 Score: 260
Period size: 44 Copynumber: 8.5 Consensus size: 42
1364005 ATCTACTCTG
* * *
1364015 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-CTTT-TTTCAATCTGCTCCA
* * * * * *
1364059 CTGTAACTTCAGGGAGATAGGATAGTGTTTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGAT-CTTTTTTCAATCTGCTCCA
* * *
1364102 CTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCT-TT-TTTCAATCTGCTCCA
* * * * * * * *
1364146 CTATAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGAT-CTTTTTTCAATCTGCTCCA
* * *
1364189 CTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCT-TT-TTTCAATCTGCTCCA
* * * * * * * *
1364233 CTATAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGAT-CTTTTTTCAATCTGCTCCA
* **
1364276 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCT-T-TTTTCAATCTGCTCCA
* * ** *
1364320 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCT----TTTTTCAATCTGCTCCA
1364366 CTGTAACCTCAGGGAGATAAGA
1 CTGTAACCTCAGGGAGATAAGA
1364388 CCTGTATAAT
Statistics
Matches: 250, Mismatches: 68, Indels: 20
0.74 0.20 0.06
Matches are distributed among these distances:
42 3 0.01
43 91 0.36
44 120 0.48
45 2 0.01
46 33 0.13
47 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
CTGTAACCTCAGGGAGATAAGATCTTTTTTCAATCTGCTCCA
Found at i:1364119 original size:87 final size:87
Alignment explanation
Indices: 1364003--1364338 Score: 539
Period size: 87 Copynumber: 3.9 Consensus size: 87
1363993 AGACTTGATG
* * * * *
1364003 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC-TTATTTTAATCCGCTCCACTATAACT
*
1364067 TCAGGGAGATAGGATAGTGTTTT
65 TCAGGGAGATAGGATAGTGTCTT
1364090 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTATAACTT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTATAACTT
1364155 CAGGGAGATAGGATAGTGTCTT
66 CAGGGAGATAGGATAGTGTCTT
1364177 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTATAACTT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTATAACTT
1364242 CAGGGAGATAGGATAGTGTCTT
66 CAGGGAGATAGGATAGTGTCTT
*** * * * *
1364264 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTATAACTT
1364329 CAGGGAGATA
66 CAGGGAGATA
1364339 AGATCTGAAA
Statistics
Matches: 235, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
87 234 1.00
88 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTATAACTT
CAGGGAGATAGGATAGTGTCTT
Found at i:1364221 original size:174 final size:174
Alignment explanation
Indices: 1364003--1364387 Score: 540
Period size: 174 Copynumber: 2.2 Consensus size: 174
1363993 AGACTTGATG
* *
1364003 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAACTT
* * *
1364068 CAGGGAGATAGGATAGTGTTTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATT
66 CAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACT
* *
1364133 TTAATCCGCTCCACTATAACTTCAGGGAGATAGGATAGTGTCTT
131 TCAATCCGCTCCACTATAACCTCAGGGAGATAGGATAGTGTCTT
* * *
1364177 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTCTTATTTTAATCCGCTCCACTATAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTATAACT
*
1364241 TCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGC
65 TCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGAC
* * * * *
1364306 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTC
130 TTCAATCCGCTCCACTATAACCTCAGGGAGATAGGATAGTG----TCTT
* * *
1364354 CGGTCTACTCCACTGTAACCTCAGGGAGATAAGA
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGA
1364388 CCTGTATAAT
Statistics
Matches: 186, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
173 4 0.02
174 149 0.80
177 33 0.18
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (174 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAACTT
CAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACT
TCAATCCGCTCCACTATAACCTCAGGGAGATAGGATAGTGTCTT
Found at i:1373113 original size:46 final size:46
Alignment explanation
Indices: 1373041--1373136 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
1373031 CATACTTCAA
*
1373041 ACTTAATAGATCAGCCTGAACTGCTAGAGTTTGCAGATGATCAGCT
1 ACTTAATAGATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCT
1373087 ACTTAATAGATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCT
1 ACTTAATAGATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCT
1373133 ACTT
1 ACTT
1373137 CGCGCACTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (46 bp):
ACTTAATAGATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCT
Found at i:1373482 original size:42 final size:42
Alignment explanation
Indices: 1373434--1373527 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
1373424 ACTAGTAGAC
*
1373434 TCTTTCCCAAGGCGACTTCTCGAGCTCGAGTATCCTGAAATT
1 TCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCTGAAATT
1373476 TCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCTGAAATT
1 TCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCTGAAATT
1373518 TCTTTTCCCA
1 TC-TTTCCCA
1373528 TTGATTAGCT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 43 0.86
43 7 0.14
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.32
Consensus pattern (42 bp):
TCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCTGAAATT
Found at i:1385046 original size:16 final size:17
Alignment explanation
Indices: 1385025--1385056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1385015 CAACTAATTT
1385025 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
1385041 TAATTTTAATTAAAAA
1 TAATTTTAATTAAAAA
1385057 TGGGCCGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:1385239 original size:21 final size:22
Alignment explanation
Indices: 1385215--1385256 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1385205 AACCAAAGGC
*
1385215 GAATCTA-GGTGGTTGGCAGGT
1 GAATCTAGGGGGGTTGGCAGGT
1385236 GAATCTAGGGGGGTTGGCAGG
1 GAATCTAGGGGGGTTGGCAGG
1385257 CGCCCCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.10, G:0.48, T:0.24
Consensus pattern (22 bp):
GAATCTAGGGGGGTTGGCAGGT
Found at i:1386585 original size:16 final size:16
Alignment explanation
Indices: 1386566--1386599 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1386556 AGTTGATTTG
* *
1386566 ATTTTAAATTTTAATA
1 ATTTTAAACTTAAATA
1386582 ATTTTAAACTTAAATA
1 ATTTTAAACTTAAATA
1386598 AT
1 AT
1386600 CTAAATTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAACTTAAATA
Found at i:1389623 original size:25 final size:25
Alignment explanation
Indices: 1389595--1389645 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
1389585 TTCTTAATTT
1389595 TATTTAT-TTAA-ATATAATTATAAAA
1 TATTTATATTAATAT-TAA-TATAAAA
1389620 TATTTATATTAATATTAATATAAAA
1 TATTTATATTAATATTAATATAAAA
1389645 T
1 T
1389646 TATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 15 0.62
26 7 0.29
27 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTTATATTAATATTAATATAAAA
Found at i:1394252 original size:60 final size:54
Alignment explanation
Indices: 1394180--1394290 Score: 168
Period size: 54 Copynumber: 1.9 Consensus size: 54
1394170 GGGATACAAA
1394180 AAATGTGTCTGGCACAAAGTATATTTATGTTTTTTTTTTTTTTTTTTTAAGTTTTTCACT
1 AAATGTGTCTGGCAC-AA-T-T-TTT-T-TTTTTTTTTTTTTTTTTTTAAGTTTTTCACT
1394240 AAATGTGTCTGGCACAATTTTTTTTTTTTTTTTTTTTTTTTTAAGTTTTTC
1 AAATGTGTCTGGCACAATTTTTTTTTTTTTTTTTTTTTTTTTAAGTTTTTC
1394291 CATCTATTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
54 28 0.55
55 1 0.02
56 3 0.06
57 1 0.02
58 1 0.02
59 2 0.04
60 15 0.29
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (54 bp):
AAATGTGTCTGGCACAATTTTTTTTTTTTTTTTTTTTTTTTTAAGTTTTTCACT
Found at i:1394289 original size:1 final size:1
Alignment explanation
Indices: 1394257--1394281 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1394247 TCTGGCACAA
1394257 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1394282 AAGTTTTTCC
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1404972 original size:20 final size:20
Alignment explanation
Indices: 1404919--1404972 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1404909 AAAATGGGGT
*
1404919 TTAATTAAATTTTTATCAGA
1 TTAATTAAATTTTTAACAGA
* * *
1404939 TTAA-TAAGAATTTTAAGAGC
1 TTAATTAA-ATTTTTAACAGA
1404959 TTAATTAAATTTTT
1 TTAATTAAATTTTT
1404973 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (20 bp):
TTAATTAAATTTTTAACAGA
Found at i:1405269 original size:18 final size:18
Alignment explanation
Indices: 1405228--1405270 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1405218 TCTATACTTG
* *
1405228 AATCTGACTCTATGCTGA
1 AATCTAACTCTAAGCTGA
**
1405246 CGTCTAACTCTAAGCTGA
1 AATCTAACTCTAAGCTGA
1405264 AATCTAA
1 AATCTAA
1405271 TTATAAGATT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (18 bp):
AATCTAACTCTAAGCTGA
Found at i:1406764 original size:18 final size:18
Alignment explanation
Indices: 1406720--1406771 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1406710 ATTTAGGTCC
*
1406720 AAAAATTAT-TATTCTATA
1 AAAAATTATATATT-TTTA
* *
1406738 GAAATTTATATATTTTTA
1 AAAAATTATATATTTTTA
*
1406756 AAAAATTATAAATTTT
1 AAAAATTATATATTTT
1406772 GAAATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
AAAAATTATATATTTTTA
Found at i:1406798 original size:18 final size:19
Alignment explanation
Indices: 1406767--1406816 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
1406757 AAAATTATAA
*
1406767 ATTTTGAAATTTTTACAAA-T
1 ATTTTG-AA-TTTTAAAAATT
1406787 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
1406806 ATTTTG-ATTTT
1 ATTTTGAATTTT
1406817 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.46
19 9 0.32
20 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:1406798 original size:19 final size:20
Alignment explanation
Indices: 1406767--1406817 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1406757 AAAATTATAA
*
1406767 ATTTTGAAATTTTTACAAA-T
1 ATTTTG-AATTTTTAAAAATT
1406787 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
1406806 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
1406818 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:1408366 original size:14 final size:14
Alignment explanation
Indices: 1408347--1408383 Score: 60
Period size: 12 Copynumber: 2.8 Consensus size: 14
1408337 TAAATTTACA
1408347 AATTTTATCAATCT
1 AATTTTATCAATCT
1408361 AATTTTA--AATCT
1 AATTTTATCAATCT
1408373 AATTTTATCAA
1 AATTTTATCAA
1408384 ATGTATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTATCAATCT
Found at i:1409444 original size:32 final size:32
Alignment explanation
Indices: 1409407--1409483 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
1409397 ATGCATGTGT
* * **
1409407 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
1409439 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
1409471 GTAACTTTTCATA
1 GTAACTTTTCATA
1409484 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:1413702 original size:12 final size:12
Alignment explanation
Indices: 1413687--1413757 Score: 85
Period size: 12 Copynumber: 6.0 Consensus size: 12
1413677 GAAATAAAAC
1413687 AAAGAATATAAT
1 AAAGAATATAAT
1413699 AAAGAATATAAT
1 AAAGAATATAAT
1413711 GAAA-AGATA-AAT
1 -AAAGA-ATATAAT
* *
1413723 AAA-AATAAAAC
1 AAAGAATATAAT
1413734 AAAGAATATAAT
1 AAAGAATATAAT
1413746 AAAGAATATAAT
1 AAAGAATATAAT
1413758 GAAAAGAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
10 3 0.06
11 9 0.17
12 34 0.65
13 6 0.12
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.21
Consensus pattern (12 bp):
AAAGAATATAAT
Found at i:1413747 original size:47 final size:47
Alignment explanation
Indices: 1413678--1413770 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
1413668 AAATTTGAAG
*
1413678 AAATAAAACAAAGAATATAATAAAGAATATAATGAAAAGATAAATAA
1 AAATAAAACAAAGAATATAATAAAGAATATAATGAAAAGAGAAATAA
1413725 AAATAAAACAAAGAATATAATAAAGAATATAATGAAAAGAGAAATA
1 AAATAAAACAAAGAATATAATAAAGAATATAATGAAAAGAGAAATA
1413771 TTTTTTATGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (47 bp):
AAATAAAACAAAGAATATAATAAAGAATATAATGAAAAGAGAAATAA
Found at i:1414002 original size:32 final size:32
Alignment explanation
Indices: 1413965--1414041 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
1413955 ATGCATGTGT
* * **
1413965 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
1413997 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
1414029 GTAACTTTTCATA
1 GTAACTTTTCATA
1414042 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:1417545 original size:89 final size:88
Alignment explanation
Indices: 1417431--1417749 Score: 380
Period size: 89 Copynumber: 3.6 Consensus size: 88
1417421 ACCCCCCATT
* *
1417431 AAAACATTACCTGAAGCAAAAGAAACCTTTCAAGGAAACAAGAAAGGAACAAAAAGAAACCATTG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAA-GAAACAAGAAAGGAACAAAAAGAAACCATTG
* *
1417496 CATGAAATAAAAAATATCCAACTG
65 CATGAAATGAAAAATATCCAACTA
* * * * * * *
1417520 AAAACAGTACCTGAAGTAAATGAAACCTTTCAAGATAACAAGAAA--AA-GAGAAGAGA--ATGG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGA-AACAAGAAAGGAACAAAAAGAAACCATTG
* * *** * *
1417580 CATGGAATGAGAAACCCCCCA-TT
65 CATGAAATGAAAAATATCCAACTA
1417603 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAGGAACAAAAAGAAACCATTG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCC-AAGAAACAAGAAAGGAACAAAAAGAAACCATTG
1417668 CATGAAATGAAAAATATCCAACTA
65 CATGAAATGAAAAATATCCAACTA
* *
1417692 AAAACATTACCTAAAGTAAATGAAACCTTCCAAGAAAGCAAGAAAGGAACAAAAAGAA
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGAAA-CAAGAAAGGAACAAAAAGAA
1417750 CGATTGAATG
Statistics
Matches: 190, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
83 38 0.20
84 21 0.11
85 2 0.01
86 12 0.06
87 2 0.01
88 26 0.14
89 89 0.47
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.14
Consensus pattern (88 bp):
AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGAAACAAGAAAGGAACAAAAAGAAACCATTGC
ATGAAATGAAAAATATCCAACTA
Found at i:1417630 original size:172 final size:173
Alignment explanation
Indices: 1417346--1417736 Score: 642
Period size: 172 Copynumber: 2.3 Consensus size: 173
1417336 GAACCCCATC
* **
1417346 AAAACAATACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATG
1 AAAACAGTACCTAAAG-TAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATG
* *
1417411 GAATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTTCAAGGAAACAAGAAA
65 GAATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTCCAAAGAAACAAGAAA
*
1417476 GGAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTG
130 GGAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
* *
1417520 AAAACAGTACCTGAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGAGAATGGCATGG
1 AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGG
*
1417585 AATGAG-AAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAG
66 AATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTCCAAAGAAACAAGAAAG
*
1417649 GAACAAAAAGAAACCATTGCATGAAATGAAAAATATCCAACTA
131 GAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
* *
1417692 AAAACATTACCTAAAGTAAATGAAACCTTCCAAGA-AAGCAAGAAA
1 AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAA-CAAGAAA
1417737 GGAACAAAAA
Statistics
Matches: 203, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 2 0.01
172 135 0.67
173 52 0.26
174 14 0.07
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (173 bp):
AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGG
AATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTCCAAAGAAACAAGAAAG
GAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
Found at i:1423308 original size:19 final size:19
Alignment explanation
Indices: 1423284--1423342 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
1423274 TCTAATTAAG
1423284 TAATAACTCTATTTT-ACTT
1 TAATAACTCTATTTTCA-TT
* *
1423303 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
1423321 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
1423340 TAA
1 TAA
1423343 AATATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 14 0.41
19 20 0.59
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:1424203 original size:23 final size:25
Alignment explanation
Indices: 1424175--1424239 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
1424165 ATTTAATACA
**
1424175 ACAAGTTAC-T-TATTTTAATTGTG
1 ACAAGTTACATGTATTAAAATTGTG
**
1424198 ACAAGTGGCATGTATTAAAATTGTG
1 ACAAGTTACATGTATTAAAATTGTG
*
1424223 ACAAGTTACATATATTA
1 ACAAGTTACATGTATTA
1424240 CATATTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 7 0.21
24 1 0.03
25 25 0.76
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (25 bp):
ACAAGTTACATGTATTAAAATTGTG
Found at i:1429889 original size:12 final size:13
Alignment explanation
Indices: 1429865--1429893 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1429855 GGGCTATAAC
1429865 TATTGCATTTATT
1 TATTGCATTTATT
1429878 TATTGC-TTTATT
1 TATTGCATTTATT
1429890 TATT
1 TATT
1429894 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:1431484 original size:22 final size:22
Alignment explanation
Indices: 1431456--1431500 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1431446 GATCTATAGA
1431456 GATAGATCAAAACGACTACTAG
1 GATAGATCAAAACGACTACTAG
1431478 GATAGATCAAAACGACTACTAG
1 GATAGATCAAAACGACTACTAG
1431500 G
1 G
1431501 TCTAAGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (22 bp):
GATAGATCAAAACGACTACTAG
Found at i:1436108 original size:18 final size:18
Alignment explanation
Indices: 1436072--1436107 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1436062 TTTTAGTAAA
1436072 TATATATATTTATAATTT
1 TATATATATTTATAATTT
*
1436090 TATATA-ATTTTTAATTT
1 TATATATATTTATAATTT
1436107 T
1 T
1436108 TTAAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATATATTTATAATTT
Found at i:1442292 original size:18 final size:18
Alignment explanation
Indices: 1442269--1442311 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1442259 GAATGAGTTT
1442269 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
1442287 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
1442305 TTAATTA
1 TTAATTA
1442312 CACCCTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:1452866 original size:18 final size:16
Alignment explanation
Indices: 1452823--1452870 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
1452813 TTTGATTATA
*
1452823 ATATTAATATTAATTT
1 ATATAAATATTAATTT
1452839 ATATAAATATTAATTT
1 ATATAAATATTAATTT
1452855 ATAATCAAATATTAAT
1 AT-AT-AAATATTAAT
1452871 ATAAACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 17 0.59
17 2 0.07
18 10 0.34
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATATTAATTT
Found at i:1453130 original size:23 final size:23
Alignment explanation
Indices: 1453100--1453152 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1453090 AATACCCTAG
* *
1453100 CCAATTTTATTGGTCGATATGGT
1 CCAATTTTATTGGCCGAAATGGT
*
1453123 CCAATTTTATTGGCCGAAATTGT
1 CCAATTTTATTGGCCGAAATGGT
1453146 CCAATTT
1 CCAATTT
1453153 AGAGAGCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (23 bp):
CCAATTTTATTGGCCGAAATGGT
Found at i:1453251 original size:13 final size:14
Alignment explanation
Indices: 1453224--1453250 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1453214 AAGTTTAGAA
1453224 ATTTTTAAAATTTT
1 ATTTTTAAAATTTT
1453238 ATTTTTAAAATTT
1 ATTTTTAAAATTT
1453251 AAAATTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTTAAAATTTT
Found at i:1459676 original size:26 final size:26
Alignment explanation
Indices: 1459647--1459708 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1459637 TACCCTCAAC
*
1459647 AAAATTTTGACGAGTTTAC-CGTTGGT
1 AAAATTTTGACGAGTTTACTC-CTGGT
* * *
1459673 AAAACTTTGACGATTTTGCTCCTGGT
1 AAAATTTTGACGAGTTTACTCCTGGT
1459699 AAAATTTTGA
1 AAAATTTTGA
1459709 AAAAATATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (26 bp):
AAAATTTTGACGAGTTTACTCCTGGT
Found at i:1459859 original size:6 final size:6
Alignment explanation
Indices: 1459848--1459880 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1459838 ATGATTGCAA
*
1459848 ATTTCC ATTTCC ATTT-C ATTTTC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1459881 TTGAAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTCC
Found at i:1459870 original size:12 final size:12
Alignment explanation
Indices: 1459848--1459881 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1459838 ATGATTGCAA
*
1459848 ATTTCCATTTCC
1 ATTTCCATTTTC
1459860 ATTT-CATTTTC
1 ATTTCCATTTTC
1459871 ATTTCCATTTT
1 ATTTCCATTTT
1459882 TGAAAACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTCCATTTTC
Found at i:1459873 original size:17 final size:17
Alignment explanation
Indices: 1459848--1459880 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1459838 ATGATTGCAA
1459848 ATTTCCATTTCCATTTC
1 ATTTCCATTTCCATTTC
*
1459865 ATTTTCATTTCCATTT
1 ATTTCCATTTCCATTT
1459881 TTGAAAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTCCATTTCCATTTC
Found at i:1463898 original size:8 final size:8
Alignment explanation
Indices: 1463885--1463957 Score: 58
Period size: 8 Copynumber: 8.9 Consensus size: 8
1463875 TTTTGAAAAT
1463885 TAAATTTA
1 TAAATTTA
*
1463893 TAAATTTT
1 TAAATTTA
**
1463901 TAGTTTTTA
1 TA-AATTTA
*
1463910 TATATTTA
1 TAAATTTA
*
1463918 TACATTTA
1 TAAATTTA
*
1463926 TACATTTATA
1 TA-AATT-TA
1463936 TAAATTTA
1 TAAATTTA
1463944 TAAA-TTA
1 TAAATTTA
1463951 TAAATTT
1 TAAATTT
1463958 TATATTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
7 7 0.13
8 31 0.60
9 10 0.19
10 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (8 bp):
TAAATTTA
Found at i:1463944 original size:26 final size:24
Alignment explanation
Indices: 1463885--1464032 Score: 70
Period size: 25 Copynumber: 5.9 Consensus size: 24
1463875 TTTTGAAAAT
* * *
1463885 TAAATTTATAAATTTTTAGTTTTTA
1 TAAATTTAT-AATTTATAATTTATA
*
1463910 TATATTTATACATTTATACATTTATA
1 TAAATTTATA-ATTTATA-ATTTATA
*
1463936 TAAATTTATAAATTATAAATTT-TA
1 TAAATTTATAATTTAT-AATTTATA
** * *
1463960 TATTTTTAAAATATTGTAGGATTT-TA
1 TAAATTTATAAT-TTATA--ATTTATA
* *
1463986 TATAATTT-TAATTGTATACGTTTTTA
1 TA-AATTTATAATT-TATA-ATTTATA
1464012 TAAATTTAT-ATTTATATATTT
1 TAAATTTATAATTTATA-ATTT
1464033 CAAACTAATT
Statistics
Matches: 94, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
24 19 0.20
25 38 0.40
26 34 0.36
27 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TAAATTTATAATTTATAATTTATA
Found at i:1464013 original size:24 final size:25
Alignment explanation
Indices: 1463981--1464027 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1463971 TATTGTAGGA
*
1463981 TTTTATATAATTTTA-ATTGTATACG
1 TTTTATATAAATTTATATT-TATACG
1464006 TTTT-TATAAATTTATATTTATA
1 TTTTATATAAATTTATATTTATA
1464028 TATTTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTATATAAATTTATATTTATACG
Found at i:1466663 original size:25 final size:25
Alignment explanation
Indices: 1466615--1466663 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1466605 CTAGGTTAAT
* **
1466615 TAAAGTTTAAATGGGAAACTAAAAA
1 TAAAGTTTAAATAGGAAAAGAAAAA
*
1466640 TAAAGTTTAACTAGGAAAAGAAAA
1 TAAAGTTTAAATAGGAAAAGAAAA
1466664 GACAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.22
Consensus pattern (25 bp):
TAAAGTTTAAATAGGAAAAGAAAAA
Found at i:1471075 original size:28 final size:31
Alignment explanation
Indices: 1471043--1471101 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
1471033 TGTTTTGTTT
1471043 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
1471071 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
1471102 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:1474027 original size:17 final size:17
Alignment explanation
Indices: 1474005--1474077 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 17
1473995 TTTTCTATTA
1474005 ATTAAATAAAATTTAAT
1 ATTAAATAAAATTTAAT
** *
1474022 ATTAAATTTAATCTAAT
1 ATTAAATAAAATTTAAT
* *
1474039 ATT-TATCAAAA-TAAAT
1 ATTAAAT-AAAATTTAAT
* * *
1474055 ATTAGATTAAATTTAGT
1 ATTAAATAAAATTTAAT
1474072 ATTAAA
1 ATTAAA
1474078 ATGATTAAGT
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
16 11 0.28
17 29 0.73
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTAAATAAAATTTAAT
Found at i:1477904 original size:6 final size:6
Alignment explanation
Indices: 1477889--1477928 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
1477879 GCATTACAAA
*
1477889 AAAAAGG AAAAAG AAAAAG AAAAAG AAAAAG AAAAGG AAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
1477929 TAAATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1483552 original size:27 final size:27
Alignment explanation
Indices: 1483522--1483577 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1483512 AGTTCGAGAG
* *
1483522 CAATGAAGCGTCAACGAAGTGGACCAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
**
1483549 CAATGATTCGTCAACGAAGCGGAACAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
1483576 CA
1 CA
1483578 TCGAAACACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CAATGAAGCGTCAACGAAGCGGAACAT
Found at i:1503196 original size:92 final size:91
Alignment explanation
Indices: 1503039--1503247 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
1503029 TTGATTTTAG
* * *
1503039 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
1503104 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
1503131 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
1503195 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
1503223 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
1503248 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:1503210 original size:24 final size:25
Alignment explanation
Indices: 1503175--1503222 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1503165 TTATGAAATT
1503175 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
1503199 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
1503223 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:1503376 original size:66 final size:61
Alignment explanation
Indices: 1503301--1503511 Score: 170
Period size: 66 Copynumber: 3.4 Consensus size: 61
1503291 AAATATATTT
1503301 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATAA
1503366 G
61 G
* * * * **
1503367 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATTA-T-AA-TATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
*
1503421 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATA
1503485 AG
60 AG
*
1503487 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
1503512 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 9 0.08
66 32 0.28
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (61 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
Found at i:1503401 original size:120 final size:120
Alignment explanation
Indices: 1503263--1503555 Score: 484
Period size: 120 Copynumber: 2.4 Consensus size: 120
1503253 AATTATTTTA
* *
1503263 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTAT-AT
* * *
1503325 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
*
1503383 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1503448 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
1503503 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1503556 TAAATATGAT
Statistics
Matches: 163, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
119 6 0.04
120 155 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAG
Found at i:1503423 original size:15 final size:15
Alignment explanation
Indices: 1503388--1503439 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1503378 TTAAGAATTT
*
1503388 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1503402 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1503416 TATTTAATAATAAT-
1 TATTTAATTATAATA
1503430 TATGTTAATT
1 TAT-TTAATT
1503440 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1503532 original size:18 final size:17
Alignment explanation
Indices: 1503504--1503538 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1503494 ATTATTAAGA
*
1503504 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1503521 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1503539 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1503795 original size:16 final size:16
Alignment explanation
Indices: 1503774--1503825 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
1503764 GATTTGCTAT
1503774 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1503790 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
1503806 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
1503822 TACA
1 TACA
1503826 GCGAACCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1504998 original size:3 final size:3
Alignment explanation
Indices: 1504990--1505039 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1504980 AAATGCAATG
* *
1504990 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ACTA ATTA ATT TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA
1505036 ATA A
1 ATA A
1505040 AGTAACCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1505742 original size:17 final size:17
Alignment explanation
Indices: 1505716--1505754 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1505706 AGAGATCGAA
*
1505716 AAAAATGAAATAAGAAC
1 AAAAACGAAATAAGAAC
1505733 AAAAACGAAATAAGAAC
1 AAAAACGAAATAAGAAC
1505750 AAAAA
1 AAAAA
1505755 GGTTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.08, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAAACGAAATAAGAAC
Found at i:1510326 original size:25 final size:25
Alignment explanation
Indices: 1510298--1510352 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1510288 TGGATATGCT
1510298 ATTCTGATTCTGAAAATGAAATGTC
1 ATTCTGATTCTGAAAATGAAATGTC
* *
1510323 ATTCTGATTCTGAAAGTGACATGTC
1 ATTCTGATTCTGAAAATGAAATGTC
1510348 ATTCT
1 ATTCT
1510353 AATTTGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (25 bp):
ATTCTGATTCTGAAAATGAAATGTC
Found at i:1515470 original size:18 final size:20
Alignment explanation
Indices: 1515428--1515474 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
1515418 ACTTTTAAAA
*
1515428 TTTTAACTTTCTTTATATAT
1 TTTTAAATTTCTTTATATAT
*
1515448 TTTTAAATTT-TTT-TATTT
1 TTTTAAATTTCTTTATATAT
1515466 TTTTAAATT
1 TTTTAAATT
1515475 ATAAAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
20 9 0.36
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAAATTTCTTTATATAT
Found at i:1515510 original size:19 final size:19
Alignment explanation
Indices: 1515473--1515531 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1515463 TTTTTTTAAA
* *
1515473 TTATAAA-ATTTGGAGTTT
1 TTATAAATATTTTGAATTT
1515491 TTATAAATATTTTGAATTT
1 TTATAAATATTTTGAATTT
*
1515510 TTGA-AAATTATTTTAAATTT
1 TT-ATAAA-TATTTTGAATTT
1515530 TT
1 TT
1515532 TTTATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 14 0.40
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
TTATAAATATTTTGAATTT
Found at i:1515511 original size:20 final size:20
Alignment explanation
Indices: 1515488--1515532 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1515478 AAATTTGGAG
*
1515488 TTTTTATAAA-TATTTTGAAT
1 TTTTTA-AAATTATTTTAAAT
*
1515508 TTTTGAAAATTATTTTAAAT
1 TTTTTAAAATTATTTTAAAT
1515528 TTTTT
1 TTTTT
1515533 TTATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTAAAATTATTTTAAAT
Found at i:1523933 original size:21 final size:23
Alignment explanation
Indices: 1523886--1523933 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1523876 ATTTCAAGTG
* *
1523886 ATATTTTTTAATTTATTATATGT
1 ATATTTTTAAATATATTATATGT
1523909 -TATTTTTAAATATA-TATAT-T
1 ATATTTTTAAATATATTATATGT
1523929 ATATT
1 ATATT
1523934 AAGATTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.05
21 9 0.41
22 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATTTTTAAATATATTATATGT
Found at i:1536374 original size:5 final size:5
Alignment explanation
Indices: 1536364--1536397 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1536354 AGATGTCTTG
1536364 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGT
1 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGT
1536398 GCAGCACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.62
Consensus pattern (5 bp):
TTGTA
Found at i:1537650 original size:23 final size:23
Alignment explanation
Indices: 1537615--1537659 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1537605 CACTTAGCAT
*
1537615 TTTTAGCTCAATATGTAT-TAATA
1 TTTTACCTCAATAT-TATATAATA
*
1537638 TTTTACCTTAATATTATATAAT
1 TTTTACCTCAATATTATATAAT
1537660 GCAATATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTACCTCAATATTATATAATA
Found at i:1539950 original size:25 final size:25
Alignment explanation
Indices: 1539891--1539938 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1539881 GGTAGGATAT
* *
1539891 GATATGTTATGCTATGATTTGATTC
1 GATATGATATGCTATGATCTGATTC
*
1539916 GATATGATATGCTATGGTCTGAT
1 GATATGATATGCTATGATCTGAT
1539939 CTGATCTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (25 bp):
GATATGATATGCTATGATCTGATTC
Found at i:1539950 original size:30 final size:30
Alignment explanation
Indices: 1539886--1539943 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1539876 ATGGGGGTAG
* *
1539886 GATATGATATGTTATGCTATGATTTGATTC
1 GATATGATATGCTATGCTATGATCTGATTC
* *
1539916 GATATGATATGCTATGGTCTGATCTGAT
1 GATATGATATGCTATGCTATGATCTGAT
1539944 CTGATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (30 bp):
GATATGATATGCTATGCTATGATCTGATTC
Found at i:1542082 original size:12 final size:12
Alignment explanation
Indices: 1542065--1542089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1542055 TTTACATGTG
1542065 TTTAAATTTTCA
1 TTTAAATTTTCA
1542077 TTTAAATTTTCA
1 TTTAAATTTTCA
1542089 T
1 T
1542090 CGTTTATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAATTTTCA
Found at i:1545552 original size:126 final size:127
Alignment explanation
Indices: 1545325--1545557 Score: 312
Period size: 126 Copynumber: 1.8 Consensus size: 127
1545315 GTTTGTGAAA
* *
1545325 TAAGCGCCGCGAAAGAACACTACTTTTAGCGGCGTTTTCTTCCTAAGCGCAGCTAAAGATCATGT
1 TAAGCGCCGCGAAAGAACACTACTTTTAGCGGCGTTTTCTTCCTAAGCGCAGCTAAAGAACATGA
**
1545390 TCTTTAGCGGCGTTTTCTCCAAAGCGTTGCTAAAGAACATGATCTTCAGCGACGTTTTTCCC
66 TCTTTAGCGGCGTTTTCTCCAAAGCGCCGCTAAAGAACATGATCTTCAGCGACGTTTTTCCC
* *
1545452 TAAGCGCCGCTG-AAGAACA-TGA-TCTTTAGCGGCGTTTT-TTCCTAAGCGCCGCTGAAGAACA
1 TAAGCGCCGC-GAAAGAACACT-ACT-TTTAGCGGCGTTTTCTTCCTAAGCGCAGCTAAAGAACA
* *** *
1545513 TGATCTTTAGCGGCGTTTTTTCGGTAGCGCCGCTGAAGAACATGA
63 TGATCTTTAGCGGCGTTTTCTCCAAAGCGCCGCTAAAGAACATGA
1545558 GCTTTAGCAG
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
126 59 0.64
127 32 0.35
128 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (127 bp):
TAAGCGCCGCGAAAGAACACTACTTTTAGCGGCGTTTTCTTCCTAAGCGCAGCTAAAGAACATGA
TCTTTAGCGGCGTTTTCTCCAAAGCGCCGCTAAAGAACATGATCTTCAGCGACGTTTTTCCC
Found at i:1545574 original size:42 final size:42
Alignment explanation
Indices: 1545325--1545589 Score: 268
Period size: 42 Copynumber: 6.2 Consensus size: 42
1545315 GTTTGTGAAA
*
1545325 TAAGCGCCGC-GAAAGAACACT-A-CTTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTG-AAGAACA-TGATC-TTTAGCGGCGTTTT-TTCG
* * * * * *
1545368 TAAGCGCAGCTAAAGATCATGTTCTTTAGCGGCGTTTTCTCC
1 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCG
* ** * * * * *
1545410 AAAGCGTTGCTAAAGAACATGATCTTCAGCGACGTTTTTCCC
1 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCG
*
1545452 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCG
1545494 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCGG
1 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTC-G
* * *
1545537 T-AGCGCCGCTGAAGAACATGAGCTTTAGCAGCATTTTTTTCTG
1 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGC-GTTTTTTC-G
1545580 TAAGCGCCGC
1 TAAGCGCCGC
1545590 AAAAGTTAAC
Statistics
Matches: 190, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
42 142 0.75
43 39 0.21
44 9 0.05
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (42 bp):
TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCG
Found at i:1547132 original size:31 final size:29
Alignment explanation
Indices: 1547097--1547168 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 29
1547087 TTTTTGTACC
*
1547097 AAAATGAAAGCAATCC-AAAAGTTGGGTGACT
1 AAAATGAAAGC--TCCTAAAAGTTGAGTGA-T
1547128 AAAATGAAAGCTCCTTAAAAGTTGAGTGAT
1 AAAATGAAAGCTCC-TAAAAGTTGAGTGAT
1547158 AAAATTGAAAG
1 AAAA-TGAAAG
1547169 GATTTTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 3 0.08
30 5 0.14
31 29 0.78
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (29 bp):
AAAATGAAAGCTCCTAAAAGTTGAGTGAT
Found at i:1548178 original size:3 final size:3
Alignment explanation
Indices: 1548170--1548209 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1548160 GACTACAATC
1548170 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1548210 GACGGGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1551736 original size:25 final size:26
Alignment explanation
Indices: 1551685--1551736 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
1551675 GTTATAACTT
1551685 TTTTTTTATTTACCAAAAAATATATAA
1 TTTTTTTATTTACC-AAAAATATATAA
1551712 TTTTTTTATTTACC-AAAATATATAA
1 TTTTTTTATTTACCAAAAATATATAA
1551737 AAAAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.44
27 14 0.56
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTTTTATTTACCAAAAATATATAA
Found at i:1552288 original size:14 final size:14
Alignment explanation
Indices: 1552257--1552297 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1552247 CAATAACCAC
*
1552257 AATAATTGAAACTAG
1 AATAATT-AAATTAG
1552272 AATAATTAAATTAG
1 AATAATTAAATTAG
1552286 AATAATTAAATT
1 AATAATTAAATT
1552298 GATACAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (14 bp):
AATAATTAAATTAG
Found at i:1553144 original size:14 final size:14
Alignment explanation
Indices: 1553127--1553155 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1553117 TTTTTGTATC
1553127 AATTTAATTATTCT
1 AATTTAATTATTCT
1553141 AATTTAATTATTCT
1 AATTTAATTATTCT
1553155 A
1 A
1553156 GTTCCAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:1553637 original size:27 final size:27
Alignment explanation
Indices: 1553564--1553640 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
1553554 ATAACACGAG
**
1553564 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
1553591 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
1553618 TGGTGCCGCCAACAGTGTTCCCT
1 TGGTGCCGCCAACAGGGTTCCCT
1553641 CCACCCAGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:1553732 original size:23 final size:23
Alignment explanation
Indices: 1553704--1553750 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1553694 TATTTTTTTT
1553704 AATATATTTTGGTAAATAAAAAA
1 AATATATTTTGGTAAATAAAAAA
*
1553727 AATATATTTTGTTAAATAAAAAA
1 AATATATTTTGGTAAATAAAAAA
1553750 A
1 A
1553751 GTTATAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (23 bp):
AATATATTTTGGTAAATAAAAAA
Found at i:1557724 original size:17 final size:18
Alignment explanation
Indices: 1557702--1557737 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1557692 CCTCAATAAG
1557702 CATTTATA-AAAATCAAA
1 CATTTATATAAAATCAAA
*
1557719 CATTTATATAAACTCAAA
1 CATTTATATAAAATCAAA
1557737 C
1 C
1557738 CTTTCCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (18 bp):
CATTTATATAAAATCAAA
Found at i:1558003 original size:42 final size:41
Alignment explanation
Indices: 1557921--1558080 Score: 180
Period size: 42 Copynumber: 3.8 Consensus size: 41
1557911 AACTCGTACA
* * * *
1557921 ATGCC-ATATCCCAGATATGGTCTTACATGCTATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATC-TATATCG
** *
1557963 ATGCCAATAG-CCCAGTTATGGTCTTACACGAATCTCATATCC
1 ATGCCAAT-GTCCCAGACATGGTCTTACACGAATCT-ATATCG
*
1558005 ATGCCAATGTCCCAAACATGGTCTTACACGAATCTTATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATC-TATATCG
*
1558047 GTGCCAATGTCCCAGACATGGTCTTACACGAATC
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATC
1558081 ACATCTCAGT
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.02
42 79 0.77
43 21 0.21
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCTATATCG
Found at i:1563558 original size:29 final size:32
Alignment explanation
Indices: 1563523--1563589 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
1563513 CAATAAAAAT
*
1563523 AAAATTTATATTTAAAATATA-T-ATTA-ATG
1 AAAATTTATATTTAAAATAAATTAATTATATG
* *
1563552 AAAATTTATTTTTATAATAAATTAATTATATG
1 AAAATTTATATTTAAAATAAATTAATTATATG
1563584 AAAATT
1 AAAATT
1563590 AAATATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 18 0.56
30 1 0.03
31 4 0.12
32 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
AAAATTTATATTTAAAATAAATTAATTATATG
Found at i:1563617 original size:25 final size:25
Alignment explanation
Indices: 1563589--1563637 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1563579 ATATGAAAAT
* * *
1563589 TAAATATACATAATTTAAAAATATG
1 TAAATATAAAAAATTAAAAAATATG
*
1563614 TAAATTTAAAAAATTAAAAAATAT
1 TAAATATAAAAAATTAAAAAATAT
1563638 TGTTGAGGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAATATAAAAAATTAAAAAATATG
Found at i:1567454 original size:42 final size:43
Alignment explanation
Indices: 1567346--1567553 Score: 226
Period size: 42 Copynumber: 4.9 Consensus size: 43
1567336 AGCTCGTATA
* * ***
1567346 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCA-ACTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATA-TATCG
* * *
1567389 ATGCCACTGTCCCAAACAGGGTCTTACACAAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATATCG
*
1567431 ATGCCAATGTCCCACACATGGTCTTACACAAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATATCG
* *
1567473 ATGTCAATGTCCCAGACATGGTCTTACACATAAATC-TCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACA-AAATCAT-ATATCG
* * * *
1567517 ATGCCAACGTCCCAGACGTGGTCTTATACGAAATCAT
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCAT
1567554 GTACTGCCAT
Statistics
Matches: 141, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
42 70 0.50
43 42 0.30
44 29 0.21
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATATCG
Found at i:1572492 original size:16 final size:16
Alignment explanation
Indices: 1572471--1572534 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
1572461 TTCATACTAA
1572471 ATAAATTATATAAAAT
1 ATAAATTATATAAAAT
*
1572487 ATAAATTATATATAAT
1 ATAAATTATATAAAAT
*
1572503 ATAAA-TAGTTTAATATAT
1 ATAAATTA-TATAA-A-AT
1572521 ATAAATTATA-AAAA
1 ATAAATTATATAAAA
1572535 AAAATTCAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.08
16 24 0.60
17 3 0.08
18 8 0.20
19 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAAATTATATAAAAT
Found at i:1572934 original size:2 final size:2
Alignment explanation
Indices: 1572927--1572954 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1572917 AGCCTTCAAC
1572927 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
1572955 TCCTTTTCCT
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:1575288 original size:22 final size:24
Alignment explanation
Indices: 1575263--1575320 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
1575253 GTCTTAACAT
1575263 TTTTAATTTT-TTTAAATATTT-A
1 TTTTAATTTTATTTAAATATTTAA
*
1575285 TTTT-ATTTTATTTTAATATTTAA
1 TTTTAATTTTATTTAAATATTTAA
1575308 TATTTAATATTTA
1 T-TTTAAT-TTTA
1575321 ATATTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.17
22 14 0.47
23 2 0.07
24 3 0.10
25 2 0.07
26 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTAATTTTATTTAAATATTTAA
Found at i:1575308 original size:7 final size:7
Alignment explanation
Indices: 1575296--1575326 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1575286 TTTATTTTAT
1575296 TTTAATA
1 TTTAATA
1575303 TTTAATA
1 TTTAATA
1575310 TTTAATA
1 TTTAATA
1575317 TTTAATA
1 TTTAATA
1575324 TTT
1 TTT
1575327 TTATATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAATA
Found at i:1575322 original size:21 final size:20
Alignment explanation
Indices: 1575288--1575326 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1575278 ATATTTATTT
*
1575288 TATTTTATTTTAATATTTAA
1 TATTTAATTTTAATATTTAA
1575308 TATTTAATATTTAATATTT
1 TATTTAAT-TTTAATATTT
1575327 TTATATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTAATTTTAATATTTAA
Found at i:1576817 original size:13 final size:12
Alignment explanation
Indices: 1576795--1576831 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1576785 TCTCAACCTG
1576795 TATTAATTTTTTA
1 TATT-ATTTTTTA
1576808 TATTATTTTTTA
1 TATTATTTTTTA
*
1576820 TATAATTTTTTA
1 TATTATTTTTTA
1576832 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:1577507 original size:17 final size:17
Alignment explanation
Indices: 1577485--1577548 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
1577475 AATCTTAGAG
1577485 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
1577502 TTCTAATTGTGTCTTAAAG-
1 TTCTAA-T-TGT-ATACAGC
1577521 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
1577538 TTTTAATTGTA
1 TTCTAATTGTA
1577549 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 19 0.50
18 2 0.05
19 9 0.24
20 4 0.11
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:1577524 original size:36 final size:36
Alignment explanation
Indices: 1577477--1577547 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1577467 GATTATATAA
*
1577477 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
*
1577513 TCTTAAAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGT
1577548 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:1577817 original size:48 final size:48
Alignment explanation
Indices: 1577742--1577836 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
1577732 TGAGGGAATT
* *
1577742 CTGTTGAATCCTTTATCATTGTAAGTTAGGCCGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTG
* *
1577790 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTT
1577837 AAGCAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTG
Found at i:1578136 original size:42 final size:42
Alignment explanation
Indices: 1578089--1578172 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
1578079 ATTGATGATG
1578089 TCGATGATAGGCTCCATGATGGATTGCAGTCCATGCAGGAGC
1 TCGATGATAGGCTCCATGATGGATTGCAGTCCATGCAGGAGC
*
1578131 TCGATGATAGGCTCCATGATGGATTGCAGTCCATGTAGGAGC
1 TCGATGATAGGCTCCATGATGGATTGCAGTCCATGCAGGAGC
1578173 AGCTCAAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (42 bp):
TCGATGATAGGCTCCATGATGGATTGCAGTCCATGCAGGAGC
Found at i:1582941 original size:48 final size:48
Alignment explanation
Indices: 1582866--1582960 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
1582856 TGAGGGAATT
*
1582866 CTGTTAAATCCTTTATCATAGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTAAATCCTTTATCATAGCAAGTTAAGCTGACTTAGGCGTTTTTG
* * *
1582914 CTGTTGAATCCTTTATCATTGCGAGTTAAGCTGACTTAGGCGTTTTT
1 CTGTTAAATCCTTTATCATAGCAAGTTAAGCTGACTTAGGCGTTTTT
1582961 AAGTAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (48 bp):
CTGTTAAATCCTTTATCATAGCAAGTTAAGCTGACTTAGGCGTTTTTG
Found at i:1583572 original size:2 final size:2
Alignment explanation
Indices: 1583565--1583604 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1583555 CATGTCTCTT
1583565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1583605 CTTACACTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1584058 original size:11 final size:11
Alignment explanation
Indices: 1584042--1584167 Score: 64
Period size: 11 Copynumber: 12.2 Consensus size: 11
1584032 TTTTTATTTT
1584042 AAAAATTTTAA
1 AAAAATTTTAA
*
1584053 AAAAA-TTAAA
1 AAAAATTTTAA
1584063 AAAATTATTTTAA
1 AAAA--ATTTTAA
*
1584076 AAATATTTT--
1 AAAAATTTTAA
1584085 -AAAA--TTAA
1 AAAAATTTTAA
1584093 AAAAA--TTAA
1 AAAAATTTTAA
1584102 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
1584115 AAATATTTT--
1 AAAAATTTTAA
1584124 -AAAA--TTAA
1 AAAAATTTTAA
1584132 AAAAA-TTTAA
1 AAAAATTTTAA
1584142 AAAATTATTTTAA
1 AAAA--ATTTTAA
*
1584155 AAATATTTTAA
1 AAAAATTTTAA
1584166 AA
1 AA
1584168 TTAAAAAAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 34
0.69 0.05 0.26
Matches are distributed among these distances:
6 4 0.04
8 6 0.07
9 16 0.18
10 16 0.18
11 25 0.27
12 2 0.02
13 22 0.24
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:1584076 original size:32 final size:31
Alignment explanation
Indices: 1584035--1584100 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1584025 CGGCCCATTT
1584035 TTATTTTAAAAAT-TTTAAAAAAATTAAAAAAA
1 TTATTTTAAAAATATTT--AAAAATTAAAAAAA
*
1584067 TTATTTTAAAAATATTTTAAAATTAAAAAAA
1 TTATTTTAAAAATATTTAAAAATTAAAAAAA
1584098 TTA
1 TTA
1584101 AAAAAGTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 16 0.50
32 13 0.41
33 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TTATTTTAAAAATATTTAAAAATTAAAAAAA
Found at i:1584103 original size:8 final size:9
Alignment explanation
Indices: 1584085--1584184 Score: 51
Period size: 9 Copynumber: 10.3 Consensus size: 9
1584075 AAAATATTTT
1584085 AAAATTAAA
1 AAAATTAAA
1584094 AAAATTAAA
1 AAAATTAAA
1584103 AAAGTATTTTAAA
1 AAA--A--TTAAA
* **
1584116 AATATT-TT
1 AAAATTAAA
1584124 AAAATTAAA
1 AAAATTAAA
1584133 AAAATTTAAA
1 AAAA-TTAAA
1584143 AAATTATTTTAAA
1 AAA--A--TTAAA
* **
1584156 AATATT-TT
1 AAAATTAAA
1584164 AAAATTAAA
1 AAAATTAAA
1584173 AAAATTAAA
1 AAAATTAAA
1584182 AAA
1 AAA
1584185 GTATGTCAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
8 10 0.14
9 32 0.46
10 8 0.12
11 3 0.04
12 1 0.01
13 15 0.22
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (9 bp):
AAAATTAAA
Found at i:1584111 original size:39 final size:39
Alignment explanation
Indices: 1584049--1584216 Score: 282
Period size: 39 Copynumber: 4.3 Consensus size: 39
1584039 TTTAAAAATT
*
1584049 TTAAAAAAATTAAAAAAATTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAA
1584089 TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
*
1584128 TTAAAAAAATTTAAAAAATTATTTTAAAAATATTTTAAAA
1 TTAAAAAAA-TTAAAAAAGTATTTTAAAAATATTTTAAAA
* *
1584168 TTAAAAAAATTAAAAAAGTATGTCAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
1584207 TTAAAAAAAT
1 TTAAAAAAAT
1584217 AAATATATTT
Statistics
Matches: 122, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 73 0.60
40 49 0.40
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (39 bp):
TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:1584132 original size:79 final size:79
Alignment explanation
Indices: 1584049--1584216 Score: 309
Period size: 79 Copynumber: 2.1 Consensus size: 79
1584039 TTTAAAAATT
* *
1584049 TTAAAAAAATTAAAAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTTA
1 TTAAAAAAATTAAAAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATGTCA
1584114 AAAATATTTTAAAA
66 AAAATATTTTAAAA
*
1584128 TTAAAAAAATTTAAAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATGTCA
1 TTAAAAAAATTAAAAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATGTCA
1584193 AAAATATTTTAAAA
66 AAAATATTTTAAAA
1584207 TTAAAAAAAT
1 TTAAAAAAAT
1584217 AAATATATTT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 86 1.00
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (79 bp):
TTAAAAAAATTAAAAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATGTCA
AAAATATTTTAAAA
Found at i:1595005 original size:21 final size:21
Alignment explanation
Indices: 1594979--1595019 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1594969 AGACGAGCAA
* *
1594979 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1595000 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1595020 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1602149 original size:125 final size:124
Alignment explanation
Indices: 1601874--1602160 Score: 448
Period size: 124 Copynumber: 2.3 Consensus size: 124
1601864 ATTTATTAAG
* * *
1601874 GAAATCGCTCCCACGTGGATGCGCTTTTGATACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGATACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
* *
1601939 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAAAAGAATTTCT
* * * *
1601998 AAAATCGCTTCCACGTGGACACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGATACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
* *
1602063 GTTTCTAAGCAAATAGTATAAAAAAGGCTTCAAGCAGGATGCTTTATCAAAAGAATTTTT
66 GTTTCTAAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAAAAGAATTTCT
* *
1602123 GAAATTGCTCCCACGTGGATATGCTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGATACGCTTTTGCTACAGTAG
1602161 CATGTTTGGG
Statistics
Matches: 146, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
124 76 0.52
125 70 0.48
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGATACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAAAAGAATTTCT
Found at i:1605311 original size:49 final size:49
Alignment explanation
Indices: 1605256--1605553 Score: 269
Period size: 49 Copynumber: 6.5 Consensus size: 49
1605246 TAAGAATATT
* *
1605256 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
1605305 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATG
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* * *
1605354 AACTATTTTGTATTTTATTACATC--A-AATAT-AAACTATT----TTG
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* * ** *** * *
1605395 TA-TTTTATTAAATGAAATAATATC-AA-AATATTCAAAATA---------
1 AACTATT-TTGTATTTTATTACATCAAATAATA-TCAAAATATTCAAAATA
* *
1605434 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
1605483 AACTATTTTGTATTTTATTA-ATCAAATAATATCAAAATATTCAAAATG
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1605531 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
1605554 TAATATAAAC
Statistics
Matches: 205, Mismatches: 27, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
39 10 0.05
40 16 0.08
41 17 0.08
42 5 0.02
43 1 0.00
44 5 0.02
45 7 0.03
46 5 0.02
47 1 0.00
48 46 0.22
49 92 0.45
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:1605389 original size:31 final size:31
Alignment explanation
Indices: 1605346--1605413 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1605336 ATCAAAATAT
* *
1605346 TCAAA-ATGAACTATTTTGTATTTTATTACA
1 TCAAATATAAACTATTTTGTATTTTATTAAA
1605376 TCAAATATAAACTATTTTGTATTTTATTAAA
1 TCAAATATAAACTATTTTGTATTTTATTAAA
*
1605407 TGAAATA
1 TCAAATA
1605414 ATATCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (31 bp):
TCAAATATAAACTATTTTGTATTTTATTAAA
Found at i:1605408 original size:129 final size:128
Alignment explanation
Indices: 1605250--1605708 Score: 653
Period size: 129 Copynumber: 3.6 Consensus size: 128
1605240 TATTATTAAG
*
1605250 AATATTAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
* * *
1605315 TATTTTATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATC
66 TATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATC
1605378 AAATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
1 -AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTT
1605443 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTA-ATC
65 GTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATC
**** * * * * * ***
1605506 AA-AT-AA-TA-TCAAAATATTCA--AAATGAACTATTTTGTATTTTATTACATTAATATAAACT
1 AATATAAACTATTTTGTAT-TTTATTAAATGAAATAATAT-CAAAATATT-CA--AA-ATAAACT
1605565 ATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTA
60 ATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTA
*
1605630 CATT
125 CATC
1605634 AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1605699 TATTTTATTA
66 TATTTTATTA
1605709 CATTAATATA
Statistics
Matches: 288, Mismatches: 29, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
122 11 0.04
123 8 0.03
124 7 0.02
125 2 0.01
126 4 0.01
127 74 0.26
128 30 0.10
129 124 0.43
130 2 0.01
131 7 0.02
132 8 0.03
133 11 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (128 bp):
AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
TATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATC
Found at i:1605529 original size:48 final size:49
Alignment explanation
Indices: 1605376--1605550 Score: 316
Period size: 49 Copynumber: 3.6 Consensus size: 49
1605366 TTTTATTACA
1605376 TCAAATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATAT
1 TCAAA-ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATAT
1605426 TCAAAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATAT
1 TCAAAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATAT
*
1605475 TCAAAATAAACTATTTTGTATTTTATT-AATCAAATAATATCAAAATAT
1 TCAAAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATAT
*
1605523 TCAAAATGAACTATTTTGTATTTTATTA
1 TCAAAATAAACTATTTTGTATTTTATTA
1605551 CATTAATATA
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
48 46 0.38
49 71 0.58
50 5 0.04
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (49 bp):
TCAAAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATAT
Found at i:1605608 original size:79 final size:79
Alignment explanation
Indices: 1605480--1605967 Score: 933
Period size: 79 Copynumber: 6.2 Consensus size: 79
1605470 AATATTCAAA
* *
1605480 ATAAACTATTTTGTATTTTATT-AATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1605544 TTTATTACATTAAT
66 TTTATTACATTAAT
1605558 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1605623 TTTATTACATTAAT
66 TTTATTACATTAAT
1605637 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1605702 TTTATTACATTAAT
66 TTTATTACATTAAT
1605716 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1605781 TTTATTACATTAAT
66 TTTATTACATTAAT
1605795 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1605860 TTTATTACATTAAT
66 TTTATTACATTAAT
1605874 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1605939 TTTATTACATTAAT
66 TTTATTACATTAAT
* *
1605953 ACAAACTACTTTGTA
1 ATAAACTATTTTGTA
1605968 CAAATAAATT
Statistics
Matches: 405, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
78 22 0.05
79 383 0.95
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (79 bp):
ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
TTTATTACATTAAT
Found at i:1606382 original size:18 final size:18
Alignment explanation
Indices: 1606356--1606398 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1606346 GACTAGGAAA
* * *
1606356 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
1606374 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
1606392 AGGATAC
1 AGGATAC
1606399 GCATCTGACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:1608263 original size:22 final size:22
Alignment explanation
Indices: 1608237--1608311 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
1608227 AAATAGGAAT
1608237 TTGAGAGAATATTAGAGAGAAA
1 TTGAGAGAATATTAGAGAGAAA
*
1608259 TTGAGATAATATTAGAGAGAAA
1 TTGAGAGAATATTAGAGAGAAA
*
1608281 TTGAGAGAATATTAGTGAGAAA
1 TTGAGAGAATATTAGAGAGAAA
1608303 TTGAGAGAA
1 TTGAGAGAA
1608312 AAGATTTAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (22 bp):
TTGAGAGAATATTAGAGAGAAA
Found at i:1608312 original size:10 final size:10
Alignment explanation
Indices: 1608237--1608312 Score: 80
Period size: 10 Copynumber: 7.0 Consensus size: 10
1608227 AAATAGGAAT
1608237 TTGAGAGAATA
1 TTGAGAGAA-A
1608248 TTAGAGAGAAA
1 TT-GAGAGAAA
*
1608259 TTGAGATAATA
1 TTGAGAGAA-A
1608270 TTAGAGAGAAA
1 TT-GAGAGAAA
1608281 TTGAGAGAATA
1 TTGAGAGAA-A
*
1608292 TTAGTGAGAAA
1 TT-GAGAGAAA
1608303 TTGAGAGAAA
1 TTGAGAGAAA
1608313 AGATTTAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
10 20 0.36
11 17 0.30
12 19 0.34
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.25
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:1610126 original size:43 final size:44
Alignment explanation
Indices: 1610077--1610177 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 44
1610067 AAAATGAATA
* * *
1610077 AAATTATGAAAAT-GTAAAAAGATATATGTATGTACATATAT-AT
1 AAATTAT-AAAATAATAAAAAAATATAAGTATGTACATATATAAT
*
1610120 AAATTATAAGATATAATAAAAAAATATAAGTATGTATATATATAAAT
1 AAATTATAA-A-ATAATAAAAAAATATAAGTATGTACATATAT-AAT
1610167 AAATTATAAAA
1 AAATTATAAAA
1610178 ATATGTACGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.04
43 8 0.16
44 2 0.04
45 25 0.51
46 1 0.02
47 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (44 bp):
AAATTATAAAATAATAAAAAAATATAAGTATGTACATATATAAT
Found at i:1610215 original size:31 final size:31
Alignment explanation
Indices: 1610130--1610231 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 31
1610120 AAATTATAAG
* *
1610130 ATATAATAAAAAAATATAAGTATGTATATATAT
1 ATATATTATAAAAATAT--GTATGTATATATAT
*
1610163 AAATAAATTATAAAAATATGTACGTGTATATATAT
1 --ATATATTATAAAAATATGTA--TGTATATATAT
* *
1610198 GTATATTAT-AAAA-ATGTATGTATTTATAT
1 ATATATTATAAAAATATGTATGTATATATAT
1610227 ATATA
1 ATATA
1610232 ACGAAATTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
29 14 0.24
31 5 0.09
32 4 0.07
33 10 0.17
35 25 0.43
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (31 bp):
ATATATTATAAAAATATGTATGTATATATAT
Found at i:1610228 original size:35 final size:34
Alignment explanation
Indices: 1610139--1610232 Score: 100
Period size: 33 Copynumber: 2.7 Consensus size: 34
1610129 GATATAATAA
*
1610139 AAAAATATAAGTATGTATATATATAAATAAATTAT
1 AAAAAT-TATGTATGTATATATATAAATAAATTAT
* * ** *
1610174 AAAAA-TATGTACGTGTATATATATGTATATTAT
1 AAAAATTATGTATGTATATATATAAATAAATTAT
*
1610207 AAAAATGTATGTATTTATATATATAA
1 AAAAAT-TATGTATGTATATATATAA
1610233 CGAAATTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
33 27 0.57
35 20 0.43
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (34 bp):
AAAAATTATGTATGTATATATATAAATAAATTAT
Found at i:1610294 original size:19 final size:19
Alignment explanation
Indices: 1610266--1610302 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1610256 TAAATGAGTA
1610266 AATAACAATAATAATAATT
1 AATAACAATAATAATAATT
* *
1610285 AATAATAATAGTAATAAT
1 AATAACAATAATAATAAT
1610303 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAACAATAATAATAATT
Found at i:1611467 original size:13 final size:13
Alignment explanation
Indices: 1611449--1611473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1611439 GGGCTGAGGG
1611449 TTTTGGGTTGTTA
1 TTTTGGGTTGTTA
1611462 TTTTGGGTTGTT
1 TTTTGGGTTGTT
1611474 GTTAAGTTTG
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:0.04, C:0.00, G:0.32, T:0.64
Consensus pattern (13 bp):
TTTTGGGTTGTTA
Found at i:1612144 original size:45 final size:44
Alignment explanation
Indices: 1612088--1612280 Score: 203
Period size: 44 Copynumber: 4.3 Consensus size: 44
1612078 ACTACAGCGC
* * *
1612088 CAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTACAACTT
1 CAGGGAGATAAGATT-GCTATCTTCAGTCTGCTCCACTACAACTT
**
1612133 CAGGGAGATAAGACTTG-TATCTTCAACCTGCTCCACTACAACTT
1 CAGGGAGATAAGA-TTGCTATCTTCAGTCTGCTCCACTACAACTT
* * * *
1612177 CAGGGAGATAAGGTTTGCTTTCTTTAGTCTGCTCCACTGCAACTT
1 CAGGGAGATAA-GATTGCTATCTTCAGTCTGCTCCACTACAACTT
* * * *
1612222 TAAGGAGATAAGACTTG-TATCTTCA-ACGTGCTCCACTGCAACTT
1 CAGGGAGATAAGA-TTGCTATCTTCAGTC-TGCTCCACTACAACTT
1612266 CAGGGAGATAAGATT
1 CAGGGAGATAAGATT
1612281 CGCCATGATA
Statistics
Matches: 124, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
43 3 0.02
44 71 0.57
45 48 0.39
46 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CAGGGAGATAAGATTGCTATCTTCAGTCTGCTCCACTACAACTT
Found at i:1612172 original size:44 final size:44
Alignment explanation
Indices: 1612116--1612278 Score: 209
Period size: 44 Copynumber: 3.7 Consensus size: 44
1612106 TGTCTTCAGT
*
1612116 CTGCTCCGCTACAACTTCAGGGAGATAAGACTTGTATCTTCAAC
1 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTATCTTCAAC
** * * **
1612160 CTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTTTCTTTAGT
1 CTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TATCTTCAAC
* * *
1612205 CTGCTCCACTGCAACTTTAAGGAGATAAGACTTGTATCTTCAAC
1 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTATCTTCAAC
* *
1612249 GTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTGCTCCACTACAACTTCAGGGAGATAAGA
1612279 TTCGCCATGA
Statistics
Matches: 99, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 64 0.65
45 35 0.35
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTATCTTCAAC
Found at i:1612207 original size:89 final size:89
Alignment explanation
Indices: 1612088--1612283 Score: 293
Period size: 89 Copynumber: 2.2 Consensus size: 89
1612078 ACTACAGCGC
* * *
1612088 CAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTACAACTTCAGGGAGATAAGACTTGTAT
1 CAGGGAGATAAGATTCGCTGTCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTAT
1612153 CTTCAACCTGCTCCACTACAACTT
66 CTTCAACCTGCTCCACTACAACTT
* * * * * *
1612177 CAGGGAGATAAGGTTTGCTTTCTTTAGTCTGCTCCACTGCAACTTTAAGGAGATAAGACTTGTAT
1 CAGGGAGATAAGATTCGCTGTCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTAT
* *
1612242 CTTCAACGTGCTCCACTGCAACTT
66 CTTCAACCTGCTCCACTACAACTT
1612266 CAGGGAGATAAGATTCGC
1 CAGGGAGATAAGATTCGC
1612284 CATGATAACT
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 94 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (89 bp):
CAGGGAGATAAGATTCGCTGTCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTAT
CTTCAACCTGCTCCACTACAACTT
Done.