Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 123 of 199
Found at i:41215543 original size:40 final size:40
Alignment explanation
Indices: 41215346--41215529 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
41215336 TGAATGATGT
* * * *
41215346 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41215386 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
41215426 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41215464 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41215505 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41215530 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41215551 original size:79 final size:79
Alignment explanation
Indices: 41215398--41215562 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
41215388 GGACTAAGAT
* **
41215398 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
41215463 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41215477 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
41215540 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41215556 CCGAAGG
1 CCGAAGG
41215563 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41223302 original size:40 final size:39
Alignment explanation
Indices: 41223219--41223401 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 39
41223209 TTGAATGATG
* * * *
41223219 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
41223258 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
41223298 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
41223336 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
41223377 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
41223402 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
38 35 0.28
39 10 0.08
40 72 0.57
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41223353 original size:78 final size:80
Alignment explanation
Indices: 41223219--41223401 Score: 223
Period size: 78 Copynumber: 2.3 Consensus size: 80
41223209 TTGAATGATG
*
41223219 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
41223283 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
41223297 TTCCGGGCTAAG-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
41223359 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
41223376 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
41223402 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 57 0.63
79 19 0.21
80 13 0.14
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:41232381 original size:13 final size:14
Alignment explanation
Indices: 41232358--41232386 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41232348 AATAAATTAT
41232358 TTAATTTTAGTTAG
1 TTAATTTTAGTTAG
41232372 TTAA-TTTAGTTAG
1 TTAATTTTAGTTAG
41232385 TT
1 TT
41232387 CAGTTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTAATTTTAGTTAG
Found at i:41242681 original size:20 final size:20
Alignment explanation
Indices: 41242658--41242713 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
41242648 TCAGCTCCTC
41242658 CAGCTCTATTAAGCTCGTAT
1 CAGCTCTATTAAGCTCGTAT
* *
41242678 CAGCTC-ACTTGAGCTCGTTT
1 CAGCTCTA-TTAAGCTCGTAT
*
41242698 AAGCTCGT-TTAAGCTC
1 CAGCTC-TATTAAGCTC
41242714 AATTTAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (20 bp):
CAGCTCTATTAAGCTCGTAT
Found at i:41242702 original size:10 final size:10
Alignment explanation
Indices: 41242666--41242713 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
41242656 TCCAGCTCTA
41242666 TTAAGCTCGT
1 TTAAGCTCGT
* * **
41242676 ATCAGCTCAC
1 TTAAGCTCGT
*
41242686 TTGAGCTCGT
1 TTAAGCTCGT
41242696 TTAAGCTCGT
1 TTAAGCTCGT
41242706 TTAAGCTC
1 TTAAGCTC
41242714 AATTTAGTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (10 bp):
TTAAGCTCGT
Found at i:41242937 original size:20 final size:22
Alignment explanation
Indices: 41242894--41242939 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
41242884 TTTAAGAGTT
*
41242894 TTTAATTTGTCTTACCATGTTG
1 TTTAATTTGTCTTACCATGCTG
41242916 TTTAATTTGTC-TA-CATGCTG
1 TTTAATTTGTCTTACCATGCTG
41242936 TTTA
1 TTTA
41242940 GTCCATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 2 0.09
22 11 0.48
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.54
Consensus pattern (22 bp):
TTTAATTTGTCTTACCATGCTG
Found at i:41253546 original size:36 final size:37
Alignment explanation
Indices: 41253506--41253578 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
41253496 TCAAAAACCT
41253506 GCAAAACAAACAC-TCAA-CACTCAAAAAGAAAAATTA
1 GCAAAACAAAC-CGTCAATCACTCAAAAAGAAAAATTA
* ** *
41253542 GCAAACCTCACCGTTAATCACTCAAAAAGAAAAATTA
1 GCAAAACAAACCGTCAATCACTCAAAAAGAAAAATTA
41253579 AATTTTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 1 0.03
36 11 0.35
37 19 0.61
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.15
Consensus pattern (37 bp):
GCAAAACAAACCGTCAATCACTCAAAAAGAAAAATTA
Found at i:41260091 original size:26 final size:26
Alignment explanation
Indices: 41260062--41260211 Score: 113
Period size: 27 Copynumber: 5.6 Consensus size: 26
41260052 ATATTGAGCC
* *
41260062 CGCACACTCAGTGCTA-TACATCAACT
1 CGCACACTTAGTGCTACTA-ATCAAAT
*
41260088 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAC-TAATCAAAT
* * *
41260115 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTAC-TAATCA-AAT
** ** *
41260143 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTAC-TAATCAAAT
* * *
41260170 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTAC-TAATCAAAT
41260197 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41260212 GTACAATTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
26 14 0.14
27 64 0.63
28 24 0.24
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (26 bp):
CGCACACTTAGTGCTACTAATCAAAT
Found at i:41260119 original size:27 final size:27
Alignment explanation
Indices: 41260082--41260210 Score: 150
Period size: 27 Copynumber: 4.7 Consensus size: 27
41260072 GTGCTATACA
* * *
41260082 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAAATCGCACACTTAGTGCCACATAG
*
41260109 TCAAATCGCACACTTAGTGCTACATAG
1 TCAAATCGCACACTTAGTGCCACATAG
* * * *
41260136 TTAGACTCGCACACTTAGTGCCGCATGG
1 TCA-AATCGCACACTTAGTGCCACATAG
* *
41260164 TCAATTCGCACACTTAGTGCAACATAG
1 TCAAATCGCACACTTAGTGCCACATAG
*
41260191 TCGAATCGCACACTTAGTGC
1 TCAAATCGCACACTTAGTGC
41260211 TGTACAATTT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
27 63 0.74
28 22 0.26
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (27 bp):
TCAAATCGCACACTTAGTGCCACATAG
Found at i:41260154 original size:55 final size:54
Alignment explanation
Indices: 41260085--41260210 Score: 171
Period size: 55 Copynumber: 2.3 Consensus size: 54
41260075 CTATACATCA
* *
41260085 ACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAG
1 ACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAG
* ** * *
41260140 ACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCAACATAGTCG
1 ACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAG
*
41260194 AATCGCACACTTAGTGC
1 ACTCGCACACTTAGTGC
41260211 TGTACAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 18 0.29
55 45 0.71
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (54 bp):
ACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAG
Found at i:41265237 original size:33 final size:33
Alignment explanation
Indices: 41265200--41265265 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41265190 ATAAATACTT
41265200 AACTTAGGTAAATAAACTAAACATATGCATTAA
1 AACTTAGGTAAATAAACTAAACATATGCATTAA
41265233 AACTTAGGTAAATAAACTAAACATATGCATTAA
1 AACTTAGGTAAATAAACTAAACATATGCATTAA
41265266 CTATTCCAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (33 bp):
AACTTAGGTAAATAAACTAAACATATGCATTAA
Found at i:41268003 original size:63 final size:63
Alignment explanation
Indices: 41267904--41268029 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
41267894 CATCAGCTCA
41267904 ATTTAATTTTCATCCATGCATGTGTGCCTTTCATTGCATGTACCTTGAGAAGTTAGAAAGCTT
1 ATTTAATTTTCATCCATGCATGTGTGCCTTTCATTGCATGTACCTTGAGAAGTTAGAAAGCTT
41267967 ATTTAATTTTCATCCATGCATGTGTGCCTTTCATTGCATGTACCTTGAGAAGTTAGAAAGCTT
1 ATTTAATTTTCATCCATGCATGTGTGCCTTTCATTGCATGTACCTTGAGAAGTTAGAAAGCTT
41268030 TGGCTGAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (63 bp):
ATTTAATTTTCATCCATGCATGTGTGCCTTTCATTGCATGTACCTTGAGAAGTTAGAAAGCTT
Found at i:41271635 original size:14 final size:16
Alignment explanation
Indices: 41271606--41271638 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
41271596 ATCTAAACTT
41271606 AATTCAAAATTAAATA
1 AATTCAAAATTAAATA
41271622 AATT-AAAA-TAAATA
1 AATTCAAAATTAAATA
41271636 AAT
1 AAT
41271639 ATGGGTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTCAAAATTAAATA
Found at i:41276031 original size:20 final size:20
Alignment explanation
Indices: 41276008--41276049 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41275998 AAGGGGAATG
*
41276008 AAAATGTT-TGAGAAGTAAAT
1 AAAATGTTAT-AGAAGCAAAT
41276028 AAAATGTTATAGAAGCAAAT
1 AAAATGTTATAGAAGCAAAT
41276048 AA
1 AA
41276050 CAATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.17, T:0.26
Consensus pattern (20 bp):
AAAATGTTATAGAAGCAAAT
Found at i:41279098 original size:20 final size:22
Alignment explanation
Indices: 41279050--41279102 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
41279040 TTTTTTATCG
41279050 GTATTGATACCATATATGATAA
1 GTATTGATACCATATATGATAA
* * *
41279072 ATATTGATACCAT-TGT-ATTA
1 GTATTGATACCATATATGATAA
41279092 GTATTGATACC
1 GTATTGATACC
41279103 TACGTGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.48
21 2 0.07
22 12 0.44
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
GTATTGATACCATATATGATAA
Found at i:41281733 original size:29 final size:28
Alignment explanation
Indices: 41281693--41281747 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
41281683 CTTCGTACTC
41281693 TTTTTTTCTAATCTCAATTTTTTTTCTT
1 TTTTTTTCTAATCTCAATTTTTTTTCTT
* **
41281721 TTTTTTTCGTAATTTCCTTTTTTTTTC
1 TTTTTTTC-TAATCTCAATTTTTTTTC
41281748 AATTACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTTTTTCTAATCTCAATTTTTTTTCTT
Found at i:41290717 original size:15 final size:16
Alignment explanation
Indices: 41290693--41290725 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
41290683 AATGTTGTGT
*
41290693 AAACATAAAC-AAATA
1 AAACACAAACAAAATA
41290708 AAACACAAACAAAATA
1 AAACACAAACAAAATA
41290724 AA
1 AA
41290726 CAATCGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAACACAAACAAAATA
Found at i:41303444 original size:18 final size:18
Alignment explanation
Indices: 41303421--41303456 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41303411 TTTCACCTAC
41303421 ATTATAAGTGTGTCATAA
1 ATTATAAGTGTGTCATAA
41303439 ATTATAAGTGTGTCATAA
1 ATTATAAGTGTGTCATAA
41303457 TCTTGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
ATTATAAGTGTGTCATAA
Found at i:41305810 original size:29 final size:31
Alignment explanation
Indices: 41305762--41305820 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
41305752 ACTTACGTAC
* **
41305762 AATTTAGTGATCAATTTGT-AAC-TTTTTGA
1 AATTAAGTGATCAAAGTGTAAACATTTTTGA
41305791 AATTAAGTGATCAAAGTGTAAACATTTTTG
1 AATTAAGTGATCAAAGTGTAAACATTTTTG
41305821 TAGAAGCCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 3 0.12
31 6 0.24
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
AATTAAGTGATCAAAGTGTAAACATTTTTGA
Found at i:41309542 original size:12 final size:12
Alignment explanation
Indices: 41309525--41309558 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41309515 TTAGAGCAAT
41309525 TGCAAGAACAGA
1 TGCAAGAACAGA
**
41309537 TGCAAGCCCAGA
1 TGCAAGAACAGA
41309549 TGCAAGAACA
1 TGCAAGAACA
41309559 ACTAGAAAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (12 bp):
TGCAAGAACAGA
Found at i:41311875 original size:7 final size:7
Alignment explanation
Indices: 41311863--41311921 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
41311853 AATACAAACA
41311863 AAAAAAG
1 AAAAAAG
41311870 AAAAAAAG
1 -AAAAAAG
41311878 AAAAAAG
1 AAAAAAG
*
41311885 -AAAAGG
1 AAAAAAG
41311891 AAAAAAG
1 AAAAAAG
*
41311898 AAAATA-
1 AAAAAAG
*
41311904 AAAGAAG
1 AAAAAAG
41311911 -AAAAAG
1 AAAAAAG
41311917 AAAAA
1 AAAAA
41311922 GGAGAGGCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 14 0.33
7 21 0.50
8 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:41311875 original size:8 final size:8
Alignment explanation
Indices: 41311862--41311921 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
41311852 AAATACAAAC
41311862 AAAAAAAG
1 AAAAAAAG
41311870 AAAAAAAG
1 AAAAAAAG
41311878 -AAAAAAG
1 AAAAAAAG
41311885 ---AAAAG
1 AAAAAAAG
*
41311890 GAAAAAAG
1 AAAAAAAG
41311898 AAAATAAAAG
1 -AAA-AAAAG
41311908 AAGAAAAAG
1 AA-AAAAAG
41311917 AAAAA
1 AAAAA
41311922 GGAGAGGCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 16 0.36
9 11 0.24
10 6 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:41311881 original size:6 final size:6
Alignment explanation
Indices: 41311872--41311922 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
41311862 AAAAAAAGAA
*
41311872 AAAAAG AAAAAAG AAAAGG AAAAAAG AAAATA- AAAGAAG AAAAAG AAAAAG
1 AAAAAG -AAAAAG AAAAAG -AAAAAG AAAA-AG AAA-AAG AAAAAG AAAAAG
41311923 GAGAGGCCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 22 0.58
7 16 0.42
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:41311881 original size:13 final size:14
Alignment explanation
Indices: 41311862--41311921 Score: 61
Period size: 13 Copynumber: 4.4 Consensus size: 14
41311852 AAATACAAAC
*
41311862 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAG
41311876 AGAAAAAAG-AAAAG
1 A-AAAAAAGAAAAAG
* *
41311890 GAAAAAAG-AAAAT
1 AAAAAAAGAAAAAG
*
41311903 AAAAGAAGAAAAAG
1 AAAAAAAGAAAAAG
41311917 AAAAA
1 AAAAA
41311922 GGAGAGGCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 17 0.46
14 13 0.35
15 7 0.19
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:41311888 original size:20 final size:20
Alignment explanation
Indices: 41311865--41311921 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
41311855 TACAAACAAA
41311865 AAAAGAAAAAAAGAAAAAAG
1 AAAAGAAAAAAAGAAAAAAG
* *
41311885 AAAAGGAAAAAAG--AAAAT
1 AAAAGAAAAAAAGAAAAAAG
41311903 AAAAGAAGAAAAAGAAAAA
1 AAAAGAA-AAAAAGAAAAA
41311922 GGAGAGGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
20 12 0.39
21 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAAAGAAAAAAG
Found at i:41312433 original size:108 final size:106
Alignment explanation
Indices: 41312248--41312446 Score: 249
Period size: 108 Copynumber: 1.9 Consensus size: 106
41312238 TTCTCATCGT
* * * * * *
41312248 ATCTTAGCAAATTTGCTATCTTGATTATTTATTTATTTCGAGCTTTGTTCTCAATAAAATTCCAT
1 ATCTTAGCAAATTTGCTATCCTAATTATTTATTTAGTTCGAGCTCTGCTCTCAATAAAATTCCAC
41312313 CTTGTCCATTGTGATAATCCTTTTCATCTTATTCATTTTGA
66 CTTGTCCATTGTGATAATCCTTTTCATCTTATTCATTTTGA
* * *
41312354 ATCTTAGCAAAATTTGCTATCCTAATTAATTTCTTT-GTTCAGAGCTCTGCTCTCAATAAGATTT
1 ATCTTAGC-AAATTTGCTATCCTAATT-ATTTATTTAGTTC-GAGCTCTGCTCTCAATAAAATTC
* *
41312418 CACCTT-TCCCGTTGTGATAATCTTTTTCA
63 CACCTTGT-CCATTGTGATAATCCTTTTCA
41312447 AGCATTTTCC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
106 8 0.10
107 20 0.26
108 50 0.64
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (106 bp):
ATCTTAGCAAATTTGCTATCCTAATTATTTATTTAGTTCGAGCTCTGCTCTCAATAAAATTCCAC
CTTGTCCATTGTGATAATCCTTTTCATCTTATTCATTTTGA
Found at i:41313490 original size:46 final size:46
Alignment explanation
Indices: 41313423--41313530 Score: 191
Period size: 46 Copynumber: 2.3 Consensus size: 46
41313413 AACAAATTAA
41313423 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAG-AGGAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCA-GAGTAGATCGT
41313469 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGT
*
41313515 AGATAGTAGATCTTGT
1 AGATAGCAGATCTTGT
41313531 TAAAACGGCG
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
46 59 0.98
47 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (46 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGT
Found at i:41315766 original size:28 final size:29
Alignment explanation
Indices: 41315735--41315794 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
41315725 TTTTACCTTC
*
41315735 ATTTAATTATATGTTATTT-TTT-ATTAGA
1 ATTTAATTAT-TGTTATTTATTTAATTAAA
*
41315763 ATTTAATTATTTTTATTTATTTAATTAAA
1 ATTTAATTATTGTTATTTATTTAATTAAA
41315792 ATT
1 ATT
41315795 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.25
28 13 0.46
29 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
ATTTAATTATTGTTATTTATTTAATTAAA
Found at i:41317548 original size:31 final size:32
Alignment explanation
Indices: 41317489--41317549 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
41317479 CAGCAGCACC
* *
41317489 GTCAGGTGGAGGGCTGGCAGCAGACGACACTA
1 GTCAGGTGGAGGACTGGCAACAGACGACACTA
* *
41317521 GTCAGGTGGA-GACTGGCAATAGGCGACAC
1 GTCAGGTGGAGGACTGGCAACAGACGACAC
41317550 CACTAGTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.26, C:0.21, G:0.39, T:0.13
Consensus pattern (32 bp):
GTCAGGTGGAGGACTGGCAACAGACGACACTA
Found at i:41319674 original size:28 final size:26
Alignment explanation
Indices: 41319636--41319704 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 26
41319626 TATTCAATAC
*
41319636 ATGTTATTAATTGTGTTACTACCTCT
1 ATGTTATTAATTGTGTTACTACATCT
* ** *
41319662 ATTTTATTTTAATCATGTTATTACATCT
1 ATGTTA--TTAATTGTGTTACTACATCT
41319690 ATGTTATTAATTGTG
1 ATGTTATTAATTGTG
41319705 CAGTTCATCT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
26 12 0.36
28 21 0.64
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (26 bp):
ATGTTATTAATTGTGTTACTACATCT
Found at i:41325239 original size:34 final size:35
Alignment explanation
Indices: 41325154--41325262 Score: 130
Period size: 34 Copynumber: 3.0 Consensus size: 35
41325144 TTATAGTAAT
* *
41325154 TCGCACAAATGCCTTCGGGACTTAACCTGGATTTA
1 TCGCACAAATGCCTTCGGGACTTAACCCGGAATTA
* *
41325189 GTAACTAGCACAAATGCCTTCGGG-TTTAGCCCGGAATTA
1 -T--C--GCACAAATGCCTTCGGGACTTAACCCGGAATTA
41325228 TCGCACAAATGCCTTCGGGACTTAACCCGGAATTA
1 TCGCACAAATGCCTTCGGGACTTAACCCGGAATTA
41325263 GTATCTCGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
34 17 0.27
35 13 0.21
36 2 0.03
38 2 0.03
39 11 0.18
40 17 0.27
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (35 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGAATTA
Found at i:41325322 original size:114 final size:115
Alignment explanation
Indices: 41325119--41325338 Score: 272
Period size: 114 Copynumber: 1.9 Consensus size: 115
41325109 GCTCCTCGTT
* * *
41325119 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTGG
1 CAAATGCCTTCGGGACATAACCCGGATATAGTAATTCGCACAAAGGCCTTCGGGACTTAACCTGG
* *
41325184 ATTTAGTAACTAGCACAAATGCCTTCGGG-TTTAGCCCGGAATTATCGCA
66 ATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTATCGCA
* *
41325233 CAAATGCCTTCGGGACTTAACCCGGA-ATTAGT-ATCTCGCACAAAGGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACATAACCCGGATA-TAGTAAT-TCGCACAAAGGCCTTCGGGA-CTTA-AC
* *
41325295 C-GGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
62 CTGGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAGCCCGGA
41325339 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
113 6 0.07
114 64 0.70
115 21 0.23
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (115 bp):
CAAATGCCTTCGGGACATAACCCGGATATAGTAATTCGCACAAAGGCCTTCGGGACTTAACCTGG
ATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTATCGCA
Found at i:41325338 original size:40 final size:39
Alignment explanation
Indices: 41325119--41325338 Score: 204
Period size: 40 Copynumber: 5.7 Consensus size: 39
41325109 GCTCCTCGTT
* *
41325119 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
* * * * *
41325159 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
*
41325199 CAAATGCCTTCGGG-TTTAGCCCGGA-AT--TA-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTATTCGCA
*
41325233 CAAATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAT-TCGCA
* * * *
41325273 CAAAGGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-A-TTCGCA
41325314 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41325339 CATCATTCAA
Statistics
Matches: 149, Mismatches: 20, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
34 18 0.12
35 11 0.07
36 2 0.01
38 3 0.02
39 11 0.07
40 90 0.60
41 13 0.09
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTATTCGCA
Found at i:41329038 original size:17 final size:17
Alignment explanation
Indices: 41329016--41329055 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
41329006 CGGGTTGCAC
41329016 TAAAATTGGAGCTTCAG
1 TAAAATTGGAGCTTCAG
41329033 TAAAATTGGAGCTTCAG
1 TAAAATTGGAGCTTCAG
*
41329050 TCAAAT
1 TAAAAT
41329056 GAGTTTTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (17 bp):
TAAAATTGGAGCTTCAG
Found at i:41333372 original size:79 final size:79
Alignment explanation
Indices: 41333261--41333485 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 79
41333251 GCTCCTCGTT
** *
41333261 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-TTTAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
*
41333326 ATTTAGTAACTAGCA
65 AATTAGTAACTAGCA
41333341 CAAATGCCTTCGGGTTTAGCCCGGA-ATTAGT-ATCTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGTTTAGCCCGGATA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCG
* *
41333404 GAATTAGTATCTCGCA
64 GAATTAGTAACTAGCA
* * * * * * *
41333420 CAAAGGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGT-TTAGCCCGGATATAGT-AATTCGCACAAATGCCTTCGGGACTTAACCCG
41333484 GA
64 GA
41333486 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.02
79 67 0.53
80 46 0.37
81 9 0.07
82 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGTTTAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTAGCA
Found at i:41333445 original size:119 final size:120
Alignment explanation
Indices: 41333261--41333485 Score: 289
Period size: 119 Copynumber: 1.9 Consensus size: 120
41333251 GCTCCTCGTT
* * *
41333261 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATATAGTAATTCGCACAAAGGCCTTCGGGACTTAACCCGG
* *
41333326 ATTTAGTAAC-TAGCACAAATGCCTTCGGG-TTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* **
41333380 CAAATGCCTTCGGGACTTAACCCGGA-ATTAGT-ATCTCGCACAAAGGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACATAACCCGGATA-TAGTAAT-TCGCACAAAGGCCTTCGGGA-CTTAACC
* *
41333442 CGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 CGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
41333486 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
118 6 0.07
119 66 0.73
120 19 0.21
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAACCCGGATATAGTAATTCGCACAAAGGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:41333485 original size:40 final size:39
Alignment explanation
Indices: 41333261--41333485 Score: 226
Period size: 40 Copynumber: 5.7 Consensus size: 39
41333251 GCTCCTCGTT
* *
41333261 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
* * * *
41333301 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
*
41333341 CAAATGCCTTCGGG-TTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAT-TCGCA
*
41333380 CAAATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAT-TCGCA
* * * *
41333420 CAAAGGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-A-TTCGCA
41333461 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41333486 CATCATTCAA
Statistics
Matches: 158, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 34 0.22
40 109 0.69
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTATTCGCA
Found at i:41339902 original size:46 final size:46
Alignment explanation
Indices: 41339852--41339950 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
41339842 CAAGATTGTG
* *
41339852 TTAATTTTTTTTGAATTAATTTATTAAATTATAAAAAATGCTTGAC
1 TTAATTTTGTTTGAATTAATTTATTAAACTATAAAAAATGCTTGAC
* *
41339898 TTAATTTTGTTTGTATTAATTTATTAAACTATAACAAATGCTTGAC
1 TTAATTTTGTTTGAATTAATTTATTAAACTATAAAAAATGCTTGAC
41339944 TTAATTT
1 TTAATTT
41339951 AAATTTTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (46 bp):
TTAATTTTGTTTGAATTAATTTATTAAACTATAAAAAATGCTTGAC
Found at i:41354633 original size:14 final size:13
Alignment explanation
Indices: 41354614--41354647 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41354604 ATTGCAATAT
41354614 TTTTTTTATCGAAA
1 TTTTTTTATC-AAA
*
41354628 TTTTTTAATCAAA
1 TTTTTTTATCAAA
41354641 TTTTTTT
1 TTTTTTT
41354648 GATCCCGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (13 bp):
TTTTTTTATCAAA
Found at i:41358564 original size:51 final size:51
Alignment explanation
Indices: 41358448--41358591 Score: 151
Period size: 51 Copynumber: 3.0 Consensus size: 51
41358438 ACTCCAAAAA
* *
41358448 ATATTTGTGCCGGCCATCTCTCTCCCTCCA-CCA-AAAAAAA-AA----TT
1 ATATTGGTGCCGCCCATCTCTCTCCCTCCACCCATAAAAAAATAATTTTTT
* * ** *
41358492 ATACTGGTGTCATCCAACTCTCTCCCTCCACCCATAAAAAAATAATTTTTT
1 ATATTGGTGCCGCCCATCTCTCTCCCTCCACCCATAAAAAAATAATTTTTT
* *
41358543 ATATTGGTGCCGCCCATCTCTCTCCTTCCACCCAT-AAAAAATTATTTTT
1 ATATTGGTGCCGCCCATCTCTCTCCCTCCACCCATAAAAAAATAATTTTT
41358592 ATTATGAATA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 24 0.30
45 3 0.04
46 7 0.09
47 2 0.03
50 13 0.16
51 31 0.39
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (51 bp):
ATATTGGTGCCGCCCATCTCTCTCCCTCCACCCATAAAAAAATAATTTTTT
Found at i:41362215 original size:41 final size:41
Alignment explanation
Indices: 41362149--41362234 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
41362139 TTTAATTAGG
* * * *
41362149 TGTTTTAAATATTCCTGGACGAATTTAATTCTGCCACTACA
1 TGTTATAAATATGCCTGGACAAATTTAATACTGCCACTACA
*
41362190 TGTTATAAATATGCCTGGACAAATTTAATACTGCTACTACA
1 TGTTATAAATATGCCTGGACAAATTTAATACTGCCACTACA
41362231 TGTT
1 TGTT
41362235 TGGCCGAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGACAAATTTAATACTGCCACTACA
Found at i:41363614 original size:13 final size:13
Alignment explanation
Indices: 41363596--41363640 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
41363586 ACGAGATTGT
41363596 AAAAAAATTCAAA
1 AAAAAAATTCAAA
*
41363609 AAAAAAATT-TAA
1 AAAAAAATTCAAA
*
41363621 AAAAAAATTCGAA
1 AAAAAAATTCAAA
41363634 AAAAAAA
1 AAAAAAA
41363641 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:41366292 original size:41 final size:41
Alignment explanation
Indices: 41366230--41366315 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
41366220 TTTAATTAGG
*
41366230 TGTTTTAAATATGCCTGGACGAATTTAATGCTGCCACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
**
41366271 TGTTATAAATATGCCTGGACGAATTTAATGCTGTTACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
41366312 TGTT
1 TGTT
41366316 TGGCCGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
Found at i:41369482 original size:21 final size:21
Alignment explanation
Indices: 41369458--41369497 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41369448 CATAAATATT
*
41369458 TTTAATATATATAATAATAAA
1 TTTAAAATATATAATAATAAA
* *
41369479 TTTAAAATTTATATTAATA
1 TTTAAAATATATAATAATA
41369498 GTAATAGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAAATATATAATAATAAA
Found at i:41369872 original size:15 final size:14
Alignment explanation
Indices: 41369835--41369873 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
41369825 TAATCATTTA
41369835 AAAATTTTAAAAAAT
1 AAAATTTT-AAAAAT
*
41369850 AAACTTTTAAAAAT
1 AAAATTTTAAAAAT
41369864 AACAATTTTA
1 AA-AATTTTA
41369874 TTATAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTTTAAAAAT
Found at i:41373938 original size:25 final size:25
Alignment explanation
Indices: 41373856--41374058 Score: 78
Period size: 25 Copynumber: 8.1 Consensus size: 25
41373846 GCACACTCTC
* *
41373856 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATGA
* * * **
41373881 GAGTCATGTAACAGGAAGCTTATCC
1 GAGCCATATAACAGGAAGCTCATGA
* * *
41373906 GGGACATATATCAGGAAGCTCATGA
1 GAGCCATATAACAGGAAGCTCATGA
** * *
41373931 GAGCCATAGT--GGGGAAGCTCGTGT
1 GAGCCATA-TAACAGGAAGCTCATGA
* * *
41373955 GAG-GAAATAATAGGTAA-CTC-TGAA
1 GAGCCATATAACAGG-AAGCTCATG-A
**
41373979 GAGCCAT-TAATCAGGAAGCTCACAAA
1 GAGCCATATAA-CAGGAAGCTCA-TGA
* *
41374005 GAGCC-TTTAATCGGGAAGCTCATGAA
1 GAGCCATATAA-CAGGAAGCTCATG-A
* * *
41374031 GAGCCATATAACGGGACGCTCATAA
1 GAGCCATATAACAGGAAGCTCATGA
41374056 GAG
1 GAG
41374059 ATACGGTGTG
Statistics
Matches: 130, Mismatches: 35, Indels: 26
0.68 0.18 0.14
Matches are distributed among these distances:
22 1 0.01
23 4 0.03
24 26 0.20
25 57 0.44
26 38 0.29
27 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATGA
Found at i:41374045 original size:26 final size:26
Alignment explanation
Indices: 41373975--41374058 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
41373965 TAGGTAACTC
*
41373975 TGAAGAGCCATTAATCAGGAAGCTCA
1 TGAAGAGCCATTAATCGGGAAGCTCA
** *
41374001 CAAAGAGCCTTTAATCGGGAAGCTCA
1 TGAAGAGCCATTAATCGGGAAGCTCA
*
41374027 TGAAGAGCCATATAA-CGGGACGCTCA
1 TGAAGAGCCAT-TAATCGGGAAGCTCA
41374053 T-AAGAG
1 TGAAGAG
41374059 ATACGGTGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
25 5 0.10
26 41 0.84
27 3 0.06
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (26 bp):
TGAAGAGCCATTAATCGGGAAGCTCA
Found at i:41379356 original size:22 final size:22
Alignment explanation
Indices: 41379317--41379379 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
41379307 TCTCCGATTA
* * *
41379317 TTAGCATATTAGTACTCTCCGT
1 TTAGCACATTTGTGCTCTCCGT
*
41379339 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTTGTGCTCTCCGT
*
41379361 ATAGCAC-TTTAGTGCTCTC
1 TTAGCACATTT-GTGCTCTC
41379380 TATTTAATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 3 0.09
22 32 0.91
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTTGTGCTCTCCGT
Found at i:41379380 original size:22 final size:23
Alignment explanation
Indices: 41379325--41379380 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
41379315 TATTAGCATA
* * *
41379325 TTAGTACTCTCCGTTTAGCACAT
1 TTAGTGCTCTCTGTATAGCACAT
41379348 TT-GTGCTCTCTGTATAGCAC-T
1 TTAGTGCTCTCTGTATAGCACAT
41379369 TTAGTGCTCTCT
1 TTAGTGCTCTCT
41379381 ATTTAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (23 bp):
TTAGTGCTCTCTGTATAGCACAT
Found at i:41383349 original size:10 final size:10
Alignment explanation
Indices: 41383334--41383365 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
41383324 TGTGTATCAT
41383334 TTTTTTCTTC
1 TTTTTTCTTC
*
41383344 TTTTTTCTTT
1 TTTTTTCTTC
41383354 TTTTTTCTTC
1 TTTTTTCTTC
41383364 TT
1 TT
41383366 GTAATCAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:41388612 original size:13 final size:13
Alignment explanation
Indices: 41388588--41388653 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
41388578 AGTTCTTCAT
*
41388588 TGCTTTTTAAAAG
1 TGCTTTTGAAAAG
*
41388601 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
41388614 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
41388627 CGCTTTTGAGAAG
1 TGCTTTTGAAAAG
41388640 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
41388653 T
1 T
41388654 TTAGTTTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:41389601 original size:50 final size:50
Alignment explanation
Indices: 41389494--41389735 Score: 349
Period size: 50 Copynumber: 4.7 Consensus size: 50
41389484 ATTTGGGTAA
*
41389494 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
41389550 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
41389600 AGAGGTCACATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
41389650 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
41389700 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
41389736 TTTAGCATGT
Statistics
Matches: 174, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
50 98 0.56
51 30 0.17
53 3 0.02
55 2 0.01
56 41 0.24
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:41394187 original size:51 final size:51
Alignment explanation
Indices: 41394044--41394187 Score: 126
Period size: 51 Copynumber: 2.8 Consensus size: 51
41394034 AGCTGAAGTG
* * * * * **
41394044 GAGCAGATTAAAGTTGAGGGCAGCGAATCCTATCTCTTTGGCATTACAGTG
1 GAGCAGATTAAAGCTAAGGGCAGCGAATCTTATCTCTCTGGTATTACAGCA
* * * * * ** * * * *
41394095 GAACAGATTAAAGCTAAAGGTAGCAAACCTGGTTTCCCTGGTTTTGCAGCA
1 GAGCAGATTAAAGCTAAGGGCAGCGAATCTTATCTCTCTGGTATTACAGCA
41394146 GAGCAGATTAAAGCTAAGGGCAGCGAATCTTATCTCTCTGGT
1 GAGCAGATTAAAGCTAAGGGCAGCGAATCTTATCTCTCTGGT
41394188 GTTAAGACTG
Statistics
Matches: 66, Mismatches: 27, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (51 bp):
GAGCAGATTAAAGCTAAGGGCAGCGAATCTTATCTCTCTGGTATTACAGCA
Found at i:41394560 original size:138 final size:137
Alignment explanation
Indices: 41394308--41394737 Score: 446
Period size: 138 Copynumber: 3.2 Consensus size: 137
41394298 AGTGGAGCCG
* * * ** * * *
41394308 ATTAAAGCTGAGGGCAGCGAATC-CTATCTCTTTGGCATTTCAGTGGAACAGATTAAAGCTAAAG
1 ATTAAAGTTGAAGGCAGCAAATCTCTATCTCCCTAGCGTTACAGTGGAACAGATTAAAGCTAAAG
* *
41394372 GTAGCGAATCTTGTTTCCCTGGCGTTGTAGCGGAGCAGATTAAAGATGAAGGCAGCGAATCTTAT
66 GTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTAT
41394437 CTCCCCGGC
131 CT--CCGGC
* * * * *
41394446 GTTAAATTTGAAGGCAGCGAATCTC-AT-TGCCCTAGCGTTGCAGTGGAATAGATTAAAGCTAAA
1 ATTAAAGTTGAAGGCAGCAAATCTCTATCT-CCCTAGCGTTACAGTGGAACAGATTAAAGCTAAA
* * * ** *
41394509 AGTAGCGAATCTTGTTTCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGAA-G-TG-G------A
65 GGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTA
*
41394565 -GT--GG-
130 TCTCCGGC
* *
41394569 ATTAAAGTTGAAGGCAGCAAATC-CTATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAG
1 ATTAAAGTTGAAGGCAGCAAATCTCTATCTCCCTAGCGTTACAGTGGAACAGATTAAAGCTAAAG
* *
41394633 GTAGCAAATCTTGTTTCCCTGACGTTGCAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTAT
66 GTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTAT
41394698 CTCCTTGGC
131 CTCC--GGC
*
41394707 ATTAAAGCTGAAGGCAGCAAATCT-TATCTCC
1 ATTAAAGTTGAAGGCAGCAAATCTCTATCTCC
41394738 ATGAAGTTGC
Statistics
Matches: 236, Mismatches: 36, Indels: 40
0.76 0.12 0.13
Matches are distributed among these distances:
122 1 0.00
123 96 0.41
124 4 0.02
125 1 0.00
126 1 0.00
128 1 0.00
129 1 0.00
132 1 0.00
133 1 0.00
135 1 0.00
136 1 0.00
137 4 0.02
138 122 0.52
139 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (137 bp):
ATTAAAGTTGAAGGCAGCAAATCTCTATCTCCCTAGCGTTACAGTGGAACAGATTAAAGCTAAAG
GTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTAT
CTCCGGC
Found at i:41394564 original size:21 final size:21
Alignment explanation
Indices: 41394538--41394581 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41394528 CTGGCGTTGC
41394538 AGTGGAATAGATTAAAGCTGA
1 AGTGGAATAGATTAAAGCTGA
* * *
41394559 AGTGGAGTGGATTAAAGTTGA
1 AGTGGAATAGATTAAAGCTGA
41394580 AG
1 AG
41394582 GCAGCAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (21 bp):
AGTGGAATAGATTAAAGCTGA
Found at i:41394634 original size:261 final size:257
Alignment explanation
Indices: 41393964--41394730 Score: 1031
Period size: 258 Copynumber: 3.0 Consensus size: 257
41393954 TATTTCCTTG
* * * *
41393964 GCGTTACAGTGGAACAGATTAAAGCT-AAGGTAGCGAATTTTGTTTCCTTGGCGTTCCAATGGAA
1 GCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCC-TGGCGTTGCAGTGGAA
41394028 T-GAAATAGCTGAAGTGGAGCAGATTAAAGTTGAGGGCAGCGAATCCTATCTCTTTGGCATTACA
65 TAGAAA-AGCTGAAGTGGAGCAGATTAAAGTTGAGGGCAGCGAATCCTATCTCTTTGGCATTACA
* * ** *
41394092 GTGGAACAGATTAAAGCTAAAGGTAGCAAACCTGGTTTCCCTGGTTTTGCAGCAGAGCAGATTAA
129 GTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAA
* * * * * * *
41394157 AGCT-AAGGGCAGCGAATCTTATCTCTCTGGTGTTAAGACTGAAAGTAACCAATCTTACTTCCCT
194 AGCTGAA-GGCAGCGAATCTTATCTCCCTGGCGTTAA-ACTGAAGGCAGCAAATCTCACTTCCCT
*
41394221 G
257 A
* * *
41394222 GCGTTGTA-AGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGCAGTGGAA
1 GCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTT-CCTGGCGTTGCAGTGGAA
* * * *
41394286 TAGAATAGCTGAAGTGGAGCCGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTTCAG
65 TAGAAAAGCTGAAGTGGAGCAGATTAAAGTTGAGGGCAGCGAATCCTATCTCTTTGGCATTACAG
* *
41394351 TGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGTAGCGGAGCAGATTAAA
130 TGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAAA
* * * *
41394416 GATGAAGGCAGCGAATCTTATCTCCCCGGCGTTAAATTTGAAGGCAGCGAATCTCA-TTGCCCTA
195 GCTGAAGGCAGCGAATCTTATCTCCCTGGCGTTAAA-CTGAAGGCAGCAAATCTCACTT-CCCTA
* *
41394480 GCGTTGCAGTGGAATAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCTCTGGCGTTGCAGTGGAA
1 GCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC-CTGGCGTTGCAGTGGAA
** * * * *
41394545 TAGATTAAAGCTGAAGTGGAGTGGATTAAAGTTGAAGGCAGCAAATCCTATCTCCTTGGCGTTAC
65 TAGA--AAAGCTGAAGTGGAGCAGATTAAAGTTGAGGGCAGCGAATCCTATCTCTTTGGCATTAC
*
41394610 AGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGACGTTGCAGCGGAGCAGATTA
128 AGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTA
* *
41394675 AAGCTGAAGGCAGCGAATCTTATCTCCTTGGCATTAAAGCTGAAGGCAGCAAATCT
193 AAGCTGAAGGCAGCGAATCTTATCTCCCTGGCGTTAAA-CTGAAGGCAGCAAATCT
41394731 TATCTCCATG
Statistics
Matches: 446, Mismatches: 53, Indels: 17
0.86 0.10 0.03
Matches are distributed among these distances:
257 19 0.04
258 205 0.46
259 61 0.14
261 161 0.36
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (257 bp):
GCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCTGGCGTTGCAGTGGAAT
AGAAAAGCTGAAGTGGAGCAGATTAAAGTTGAGGGCAGCGAATCCTATCTCTTTGGCATTACAGT
GGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGCGGAGCAGATTAAAG
CTGAAGGCAGCGAATCTTATCTCCCTGGCGTTAAACTGAAGGCAGCAAATCTCACTTCCCTA
Found at i:41394639 original size:51 final size:51
Alignment explanation
Indices: 41394568--41394706 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 51
41394558 AAGTGGAGTG
* * *
41394568 GATTAAAGTTGAAGGCAGCAAATCCTATCTCCTTGGCGTTACAGTGGAACA
1 GATTAAAGCTGAAGGCAGCAAATCTTATCTCCTTGGCGTTACAGCGGAACA
* * * * * * * *
41394619 GATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGACGTTGCAGCGGAGCA
1 GATTAAAGCTGAAGGCAGCAAATCTTATCTCCTTGGCGTTACAGCGGAACA
*
41394670 GATTAAAGCTGAAGGCAGCGAATCTTATCTCCTTGGC
1 GATTAAAGCTGAAGGCAGCAAATCTTATCTCCTTGGC
41394707 ATTAAAGCTG
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (51 bp):
GATTAAAGCTGAAGGCAGCAAATCTTATCTCCTTGGCGTTACAGCGGAACA
Found at i:41394673 original size:123 final size:123
Alignment explanation
Indices: 41394231--41394683 Score: 455
Period size: 123 Copynumber: 3.6 Consensus size: 123
41394221 GGCGTTGTAA
* * * *
41394231 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGA--ATAG
1 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
** * * * * *
41394294 CTGAAGTGGAGCCGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTTCAGT
66 CTGAAGTGGAGTGGATTAAAGTTGAAGGCAGCGAATCCTATCTCCTTGGCGTTACAGT
* *
41394352 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGTAGCGGAGCAGATTAAAG
1 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
* * * * * * *
41394417 ATGAAGGCAGCGAATCTTATCTCCCCGGCGTTAAATTTGAAGGCAGCGAAT-CTCAT-TGCCCTA
66 CTGAA-G-TG-G------A-GT----GG-ATTAAAGTTGAAGGCAGCGAATCCT-ATCT-CCTTG
*
41394480 GCGTTGCAGT
114 GCGTTACAGT
* * * * *
41394490 GGAATAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCTCTGGCGTTGCAGTGGAATAGATTAAAG
1 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
*
41394555 CTGAAGTGGAGTGGATTAAAGTTGAAGGCAGCAAATCCTATCTCCTTGGCGTTACAGT
66 CTGAAGTGGAGTGGATTAAAGTTGAAGGCAGCGAATCCTATCTCCTTGGCGTTACAGT
* * *
41394613 GGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGACGTTGCAGCGGAGCAGATTAAAG
1 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
41394678 CTGAAG
66 CTGAAG
41394684 GCAGCGAATC
Statistics
Matches: 267, Mismatches: 44, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
121 54 0.20
123 103 0.39
124 6 0.02
125 1 0.00
126 1 0.00
128 1 0.00
129 1 0.00
132 1 0.00
135 1 0.00
136 1 0.00
137 5 0.02
138 92 0.34
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (123 bp):
GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAACAGATTAAAG
CTGAAGTGGAGTGGATTAAAGTTGAAGGCAGCGAATCCTATCTCCTTGGCGTTACAGT
Found at i:41396533 original size:16 final size:17
Alignment explanation
Indices: 41396512--41396551 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41396502 ATTATTTTAC
* *
41396512 TTTATTTTCTTTA-CTT
1 TTTATTTTATTTATCTG
41396528 TTTATTTTATTTATCTG
1 TTTATTTTATTTATCTG
41396545 TTTATTT
1 TTTATTT
41396552 ATGTTTGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTATTTTATTTATCTG
Found at i:41399969 original size:34 final size:34
Alignment explanation
Indices: 41399926--41399993 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41399916 GCTCACTGAC
41399926 TTGGTTCTATCGATACTTCTATGCACTTGTATCG
1 TTGGTTCTATCGATACTTCTATGCACTTGTATCG
41399960 TTGGTTCTATCGATACTTCTATGCACTTGTATCG
1 TTGGTTCTATCGATACTTCTATGCACTTGTATCG
41399994 ATAGAAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (34 bp):
TTGGTTCTATCGATACTTCTATGCACTTGTATCG
Found at i:41403051 original size:29 final size:29
Alignment explanation
Indices: 41402988--41403055 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41402978 TAATCAACCA
41402988 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41403017 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41403046 CGCACACTTA
1 CGCACACTTA
41403056 CCTTTTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41403198 original size:29 final size:30
Alignment explanation
Indices: 41403159--41403237 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
41403149 CTTAATAATC
41403159 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41403189 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
41403218 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41403238 ATCTCATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41403231 original size:176 final size:173
Alignment explanation
Indices: 41402878--41403231 Score: 512
Period size: 176 Copynumber: 2.0 Consensus size: 173
41402868 AACTCAAGGT
* *
41402878 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* * *
41402943 GAAAATATATACAGGGTTGCACGCATAATGTTTAGTAATCAACCACGCACACTTAGTGCCATGCA
66 GAAAATATATACAGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
* ***
41403008 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 CTTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
41403051 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
** * *
41403116 AGAAATATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCAT
65 AGAAA-ATATATACAGGGTT-GCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCAT
* * **
41403181 GTACTTTAAACTCGCACACTTAGTGCTGTACAATTT-AAACCCGCAC
128 GCACTTTAAACTCACACACTTAGTGCCATAC-ATTTCAAACCCGCAC
41403227 ACTTA
1 ACTTA
41403232 GTGCCAATCT
Statistics
Matches: 160, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
173 7 0.04
174 60 0.38
175 12 0.08
176 77 0.48
177 4 0.03
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATACAGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
CTTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
Found at i:41411858 original size:23 final size:23
Alignment explanation
Indices: 41411783--41411859 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 23
41411773 TATTAGAATT
41411783 TGATATTTGTTAATTCATTTTCA
1 TGATATTTGTTAATTCATTTTCA
* * * *
41411806 TGAT-TATGTTGATCTCACAAATCTT-G
1 TGATATTTGTTAAT-T--C--ATTTTCA
41411832 TGATATTTGTTAATTCATTTTCA
1 TGATATTTGTTAATTCATTTTCA
41411855 TGATA
1 TGATA
41411860 GCGTTGGGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 11 0.28
23 10 0.26
24 1 0.03
25 1 0.03
26 5 0.13
27 11 0.28
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (23 bp):
TGATATTTGTTAATTCATTTTCA
Found at i:41413319 original size:15 final size:15
Alignment explanation
Indices: 41413299--41413328 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41413289 GAAGTCTCTC
41413299 CTCCTAGTTTTTCAT
1 CTCCTAGTTTTTCAT
41413314 CTCCTAGTTTTTCAT
1 CTCCTAGTTTTTCAT
41413329 TTTTGAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.07, T:0.53
Consensus pattern (15 bp):
CTCCTAGTTTTTCAT
Found at i:41414809 original size:2 final size:2
Alignment explanation
Indices: 41414802--41414835 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41414792 GAAAACAAGC
41414802 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41414836 CTCTCAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41415127 original size:18 final size:18
Alignment explanation
Indices: 41415106--41415148 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
41415096 AATTATTTTT
41415106 AAATTTCAATTTAACCCA
1 AAATTTCAATTTAACCCA
* * *
41415124 AAATATTTATTTTTACCCA
1 AAAT-TTCAATTTAACCCA
41415143 AAATTT
1 AAATTT
41415149 ATTTAAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTCAATTTAACCCA
Found at i:41415485 original size:13 final size:13
Alignment explanation
Indices: 41415467--41415493 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41415457 AACGAACTCA
41415467 TTGATGTGAGCCC
1 TTGATGTGAGCCC
41415480 TTGATGTGAGCCC
1 TTGATGTGAGCCC
41415493 T
1 T
41415494 AATGGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (13 bp):
TTGATGTGAGCCC
Found at i:41417596 original size:30 final size:29
Alignment explanation
Indices: 41417565--41417623 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
41417555 CTTAATTATT
*
41417565 AAAAATTAAAAGTTAAAAACCTTTAAAATTA
1 AAAAAATAAAAG-TAAAAA-CTTTAAAATTA
*
41417596 AAAAAATAAAAGTAAAAATTTTAAAATT
1 AAAAAATAAAAGTAAAAACTTTAAAATT
41417624 TATTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
30 6 0.23
31 11 0.42
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAAATAAAAGTAAAAACTTTAAAATTA
Found at i:41419634 original size:19 final size:19
Alignment explanation
Indices: 41419587--41419630 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41419577 AATTAATAAA
* * *
41419587 ATTATAATTAAAGTACTAT
1 ATTAGAATTAAAATAATAT
41419606 ATTAGAATTAAAATAATAT
1 ATTAGAATTAAAATAATAT
41419625 -TTAGAA
1 ATTAGAA
41419631 ATTATTTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (19 bp):
ATTAGAATTAAAATAATAT
Found at i:41422135 original size:133 final size:135
Alignment explanation
Indices: 41421805--41422281 Score: 360
Period size: 133 Copynumber: 3.5 Consensus size: 135
41421795 GTTTTTATAT
* * * * **
41421805 GGTGTTCATGAATTTCAGTAAT-GTCATATATAATTCACATTTAGGTTTTGAAATTTAGCTCAAT
1 GGTGTTCATGAATTTCAATAATAG-CACATACAATTCGCATTTAGGTTTCAAAATTTAGCTC---
* * ** *** *
41421869 TGTACTTAAAACGTATTGTGTTGTGCTTATTATACTGTTTTTGTGTTTAATAAACATGCATTTTG
62 --TAATT-AAACG-ATTCTGTTGTATTTATTATACCACTTTCGTGTTTAATAAACATGCA-TTTG
* * *
41421934 ACTTGTGTCCATAC
122 ACTTGTTTACATAA
* * * * *
41421948 GGTGTTCGTGAATTTCAGA-AATGGCACATACACTTTGCATTTAGATTT-AGAAATTTAGCTC-A
1 GGTGTTCATGAATTTCA-ATAATAGCACATACAATTCGCATTTAGGTTTCA-AAATTTAGCTCTA
*
41422010 ATTAAACG-TTCTGTTGTATTTATTATACCACTTTCGTGTTTAATAGACATGCATTTGACTTGTT
64 ATTAAACGATTCTGTTGTATTTATTATACCACTTTCGTGTTTAATAAACATGCATTTGACTTGTT
41422074 TACATAA
129 TACATAA
* *
41422081 GGTGTTCATGAAATTCAATAATAGCACATACAATTCGCATTTAGGTTTCAAAATTTAACTCAATT
1 GGTGTTCATGAATTTCAATAATAGCACATACAATTCGCATTTAGGTTTCAAAATTTAGCTC----
* *** * * * *
41422146 GTAATTAAACGTATTCTGTTGTGTTTATTATACTGTTTTCATGTTTGATAAACATGCATGATGTC
62 -TAATTAAACG-ATTCTGTTGTATTTATTATACCACTTTCGTGTTTAATAAACATGCAT-TTGAC
* * *
41422211 TTGTTTTCACAT
124 TTGTTTACATAA
* * *
41422223 GGTGGTCATGAATTTCAATAATAG--CATACAGTTCACATTTAGGCTTTGC--AATTTAGCTC
1 GGTGTTCATGAATTTCAATAATAGCACATACAATTCGCATTTAGG-TTT-CAAAATTTAGCTC
41422282 GACCGTAATT
Statistics
Matches: 273, Mismatches: 45, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
132 1 0.00
133 65 0.24
134 38 0.14
136 5 0.02
137 3 0.01
139 9 0.03
140 26 0.10
141 42 0.15
142 35 0.13
143 48 0.18
144 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (135 bp):
GGTGTTCATGAATTTCAATAATAGCACATACAATTCGCATTTAGGTTTCAAAATTTAGCTCTAAT
TAAACGATTCTGTTGTATTTATTATACCACTTTCGTGTTTAATAAACATGCATTTGACTTGTTTA
CATAA
Found at i:41424333 original size:18 final size:17
Alignment explanation
Indices: 41424308--41424342 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41424298 TGTTAGCTTG
41424308 AACTCATTTCTTAGATT
1 AACTCATTTCTTAGATT
*
41424325 AACTCCATTTTTTAGATT
1 AACT-CATTTCTTAGATT
41424343 TGTTTTGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (17 bp):
AACTCATTTCTTAGATT
Found at i:41426228 original size:33 final size:34
Alignment explanation
Indices: 41426161--41426228 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
41426151 ATAAGATGCA
* *
41426161 ATCAAGTTTATATATTTTTAATTTTTTATTAAAT
1 ATCAAGTTTATATATTATTAATTTTTTATAAAAT
*
41426195 ATCAAGTTATTTATATTATT-ATTTTTT-TAAAAT
1 ATCAAGTT-TATATATTATTAATTTTTTATAAAAT
41426228 A
1 A
41426229 AAAAAAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 6 0.20
34 15 0.50
35 9 0.30
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (34 bp):
ATCAAGTTTATATATTATTAATTTTTTATAAAAT
Found at i:41427079 original size:16 final size:16
Alignment explanation
Indices: 41427027--41427080 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
41427017 CACAATATTT
41427027 TTATAAATATTTTAAA
1 TTATAAATATTTTAAA
* * *
41427043 TTAATTATTATATTAAA
1 TT-ATAAATATTTTAAA
*
41427060 TTATAAATATTTTTAA
1 TTATAAATATTTTAAA
41427076 TTATA
1 TTATA
41427081 TTTTATAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAAATATTTTAAA
Found at i:41428332 original size:9 final size:9
Alignment explanation
Indices: 41428318--41428346 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
41428308 ATACATAAGC
41428318 AATTTAAAA
1 AATTTAAAA
41428327 AATTTAAAA
1 AATTTAAAA
41428336 AATTTAAAA
1 AATTTAAAA
41428345 AA
1 AA
41428347 ACAATCGAAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATTTAAAA
Found at i:41439244 original size:21 final size:21
Alignment explanation
Indices: 41439218--41439262 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41439208 AAATATGGTT
*
41439218 AAAGTA-ATTCTAGACAGATTG
1 AAAGTAGATTCT-GACAGATAG
*
41439239 AAAGTAGCTTCTGACAGATAG
1 AAAGTAGATTCTGACAGATAG
41439260 AAA
1 AAA
41439263 TCCTATGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (21 bp):
AAAGTAGATTCTGACAGATAG
Found at i:41443330 original size:26 final size:26
Alignment explanation
Indices: 41443256--41443323 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
41443246 TGCCACGATC
*
41443256 GAGAAAAAGGAAGAGGGAGAAAATAG
1 GAGAAAAAAGAAGAGGGAGAAAATAG
*
41443282 GAGAAAAAAGAAGAGGGGGAAAATAG
1 GAGAAAAAAGAAGAGGGAGAAAATAG
41443308 GAGAAAAAATGAAGAG
1 GAGAAAAAA-GAAGAG
41443324 AAGAAAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 33 0.85
27 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.37, T:0.04
Consensus pattern (26 bp):
GAGAAAAAAGAAGAGGGAGAAAATAG
Found at i:41443345 original size:20 final size:20
Alignment explanation
Indices: 41443309--41443354 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
41443299 GGAAAATAGG
41443309 AGAA-AAAATGAAGAGAAGA
1 AGAAGAAAATGAAGAGAAGA
*
41443328 A-AAGAAAATGAGGAAGAAGA
1 AGAAGAAAATGAAG-AGAAGA
41443348 AGAAGAA
1 AGAAGAA
41443355 GAGGGGGCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 9 0.39
20 7 0.30
21 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.04
Consensus pattern (20 bp):
AGAAGAAAATGAAGAGAAGA
Found at i:41443908 original size:17 final size:17
Alignment explanation
Indices: 41443888--41443922 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41443878 CTTATTGTCT
*
41443888 TAGAAGTGTGTTCACAC
1 TAGAAGAGTGTTCACAC
*
41443905 TAGAGGAGTGTTCACAC
1 TAGAAGAGTGTTCACAC
41443922 T
1 T
41443923 TAAATACAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (17 bp):
TAGAAGAGTGTTCACAC
Found at i:41447300 original size:20 final size:20
Alignment explanation
Indices: 41447252--41447323 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
41447242 TCACTCATTT
*
41447252 TCAGGGGCACCATAGATGCAAA
1 TCAGGGGCACCAAAG-TGC-AA
*
41447274 ACAGGGGCACCAAAGTGCAA
1 TCAGGGGCACCAAAGTGCAA
*
41447294 TCAGGGGCA-CAAGTGTGCAA
1 TCAGGGGCACCAA-AGTGCAA
41447314 TCAGGGGCAC
1 TCAGGGGCAC
41447324 AGTTGTGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 3 0.07
20 25 0.57
21 3 0.07
22 13 0.30
ACGTcount: A:0.33, C:0.24, G:0.32, T:0.11
Consensus pattern (20 bp):
TCAGGGGCACCAAAGTGCAA
Found at i:41447324 original size:20 final size:20
Alignment explanation
Indices: 41447275--41447339 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
41447265 AGATGCAAAA
*
41447275 CAGGGGCACCAA-AGTGCAAT
1 CAGGGGCA-CAAGTGTGCAAT
41447295 CAGGGGCACAAGTGTGCAAT
1 CAGGGGCACAAGTGTGCAAT
*
41447315 CAGGGGCAC-AGTTGTGCAAA
1 CAGGGGCACAAG-TGTGCAAT
41447335 CAGGG
1 CAGGG
41447340 ACACTGAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.12
20 36 0.88
ACGTcount: A:0.31, C:0.22, G:0.35, T:0.12
Consensus pattern (20 bp):
CAGGGGCACAAGTGTGCAAT
Found at i:41450333 original size:50 final size:50
Alignment explanation
Indices: 41450273--41450391 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
41450263 CTGTCATTTT
* ** * * * *
41450273 CCAGATATGGTCTTACATGAGAGGTCTCATATCGGTGCCCATGCCATGTC
1 CCAGACATGGTCTTACATGAGACCTCTCATATCGGTACCAATGACATATC
** *
41450323 CCAGACATGGTCTTACGGGAGACCTCTCATCTCGGTACCAATGACATATC
1 CCAGACATGGTCTTACATGAGACCTCTCATATCGGTACCAATGACATATC
*
41450373 CCAGACATGCTCTTACATG
1 CCAGACATGGTCTTACATG
41450392 GGGTCTTATC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
CCAGACATGGTCTTACATGAGACCTCTCATATCGGTACCAATGACATATC
Found at i:41455337 original size:18 final size:18
Alignment explanation
Indices: 41455299--41455334 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41455289 TTATTATTTT
*
41455299 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
41455317 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
41455335 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:41455346 original size:31 final size:29
Alignment explanation
Indices: 41455309--41455374 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
41455299 TAAAATTTAC
*
41455309 TATTAAAATAA-AATTTAAATATTAAATAATT
1 TATTAAAATAATAAATT--ATATT-AATAATT
41455340 TATTAAAAATAATAAATTATATTAATAATT
1 TATT-AAAATAATAAATTATATTAATAATT
41455370 TATTA
1 TATTA
41455375 TATGATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.03
30 11 0.34
31 9 0.28
32 7 0.22
33 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TATTAAAATAATAAATTATATTAATAATT
Found at i:41456936 original size:49 final size:49
Alignment explanation
Indices: 41456873--41457001 Score: 206
Period size: 49 Copynumber: 2.7 Consensus size: 49
41456863 AATAACATGC
* * *
41456873 CAAA-GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTACTG
1 CAAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCCTGTACTG
*
41456921 CAAATGCCATATCCCAGATATGGTCTTACGTGGGATGTTTCCTGTACTG
1 CAAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCCTGTACTG
*
41456970 CAAATGCCATTTCCCAGATATGGTCTTACATG
1 CAAATGCCATATCCCAGATATGGTCTTACATG
41457002 AGAGTTCTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
48 4 0.05
49 70 0.95
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (49 bp):
CAAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCCTGTACTG
Found at i:41457043 original size:50 final size:50
Alignment explanation
Indices: 41456972--41457101 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 50
41456962 CTGTACTGCA
* * ** **
41456972 AATGCCATTTCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGAGACATCTCATATCGGCACC
* *** *
41457022 CATGCCATGTCCCAGACATGGTCTTATGGGAGACATCTCATCTCGGCACC
1 AATGCCATGTCCCAGACATGGTCTTACATGAGACATCTCATATCGGCACC
*
41457072 AACGCCATGTCCCAGACATGGTCTTACATG
1 AATGCCATGTCCCAGACATGGTCTTACATG
41457102 GGGTCTCATC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGAGACATCTCATATCGGCACC
Found at i:41457989 original size:19 final size:19
Alignment explanation
Indices: 41457956--41458003 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
41457946 TAAACAATTC
41457956 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
41457973 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
41457992 AATAATATAAAT
1 AATAATATAAAT
41458004 AGTATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:41458527 original size:18 final size:18
Alignment explanation
Indices: 41458504--41458540 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41458494 TATAGTTTGA
*
41458504 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCAAAT
*
41458522 TATTTGAGTTATTCAAAT
1 TATTTGAATTATTCAAAT
41458540 T
1 T
41458541 CGAAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCAAAT
Found at i:41458609 original size:9 final size:9
Alignment explanation
Indices: 41458592--41458622 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41458582 TCGAGTTGAT
41458592 TCGAATAAC
1 TCGAATAAC
*
41458601 TCGATTAAC
1 TCGAATAAC
41458610 TCGAATAAC
1 TCGAATAAC
41458619 TCGA
1 TCGA
41458623 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:41479001 original size:24 final size:24
Alignment explanation
Indices: 41478943--41479029 Score: 86
Period size: 24 Copynumber: 3.5 Consensus size: 24
41478933 GCTTATCCAG
* *
41478943 GCAATATAACGGGAAGCTCACAAAGA
1 GCAAT-TAACAGGTAGCTC-CAAAGA
* *
41478969 GC-CTATAACAGGTAGCTCCAGAGA
1 GCAAT-TAACAGGTAGCTCCAAAGA
*
41478993 GCAATTAACAGGTAGCTCTAAAGA
1 GCAATTAACAGGTAGCTCCAAAGA
41479017 GCAATTAATCAGG
1 GCAATTAA-CAGG
41479030 AAGCACCATA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
24 32 0.62
25 18 0.35
26 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (24 bp):
GCAATTAACAGGTAGCTCCAAAGA
Found at i:41482693 original size:25 final size:24
Alignment explanation
Indices: 41482656--41482716 Score: 95
Period size: 25 Copynumber: 2.5 Consensus size: 24
41482646 GTTTTCCAAT
*
41482656 TTTCAGCTAATATGAGCTTACCGA
1 TTTCAGCTCATATGAGCTTACCGA
41482680 TATTCAGCTCATATGAGCTTACCGA
1 T-TTCAGCTCATATGAGCTTACCGA
41482705 TTTACAGCTCAT
1 TTT-CAGCTCAT
41482717 GAGAACATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 3 0.09
25 31 0.91
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (24 bp):
TTTCAGCTCATATGAGCTTACCGA
Found at i:41482727 original size:25 final size:24
Alignment explanation
Indices: 41482656--41482731 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 24
41482646 GTTTTCCAAT
* * *
41482656 TTTCAGCTAATATGAGCTTACCGA
1 TTTCAGCTCATATGAACATACCGA
* *
41482680 TATTCAGCTCATATGAGCTTACCGA
1 T-TTCAGCTCATATGAACATACCGA
41482705 TTTACAGCTCATGA-GAACATACCGA
1 TTT-CAGCTCAT-ATGAACATACCGA
41482730 TT
1 TT
41482732 CATAGCTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.07
25 42 0.91
26 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (24 bp):
TTTCAGCTCATATGAACATACCGA
Found at i:41484597 original size:21 final size:21
Alignment explanation
Indices: 41484573--41484615 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41484563 TAGAACTCTT
41484573 ATGCGGACCTTAAAAGGTATG
1 ATGCGGACCTTAAAAGGTATG
41484594 ATGCGGACCTTAAAAGGTATG
1 ATGCGGACCTTAAAAGGTATG
41484615 A
1 A
41484616 CATTGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (21 bp):
ATGCGGACCTTAAAAGGTATG
Found at i:41486691 original size:22 final size:22
Alignment explanation
Indices: 41486657--41486747 Score: 85
Period size: 22 Copynumber: 4.2 Consensus size: 22
41486647 TTGAGGGTAG
* **
41486657 GATATGCTATGATGTGTTATAT
1 GATATGCTATGATATGAAATAT
* *
41486679 GATATGTTTTGATATGAAATAT
1 GATATGCTATGATATGAAATAT
* *
41486701 GATATGCTATGATATGAGACAT
1 GATATGCTATGATATGAAATAT
* * *
41486723 GATAT-ATTTGATATGAGATAT
1 GATATGCTATGATATGAAATAT
41486744 GATA
1 GATA
41486748 ACCTCTGATA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
21 17 0.30
22 40 0.70
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (22 bp):
GATATGCTATGATATGAAATAT
Found at i:41486759 original size:22 final size:21
Alignment explanation
Indices: 41486688--41486768 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
41486678 TGATATGTTT
* *
41486688 TGATATGAAATATGATATGCTA
1 TGATATGAGATATGATA-ACTA
* *
41486710 TGATATGAGACATGATATA-TT
1 TGATATGAGATATGATA-ACTA
*
41486731 TGATATGAGATATGATAACCTC
1 TGATATGAGATATGATAA-CTA
**
41486753 TGATATGTTATATGAT
1 TGATATGAGATATGAT
41486769 GTATGACTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 17 0.35
22 31 0.63
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (21 bp):
TGATATGAGATATGATAACTA
Found at i:41486768 original size:43 final size:44
Alignment explanation
Indices: 41486663--41486768 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
41486653 GTAGGATATG
* * **
41486663 CTATGATGTGTTATATGATATGTTTTGATATGAAATATGATATG
1 CTATGATATGTTATATGATATGATTTGATATGAAATATGATAAC
** * *
41486707 CTATGATATGAGACATGATAT-ATTTGATATGAGATATGATAAC
1 CTATGATATGTTATATGATATGATTTGATATGAAATATGATAAC
*
41486750 CTCTGATATGTTATATGAT
1 CTATGATATGTTATATGAT
41486769 GTATGACTAG
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
43 33 0.66
44 17 0.34
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.42
Consensus pattern (44 bp):
CTATGATATGTTATATGATATGATTTGATATGAAATATGATAAC
Found at i:41494452 original size:135 final size:137
Alignment explanation
Indices: 41494304--41494567 Score: 363
Period size: 136 Copynumber: 1.9 Consensus size: 137
41494294 TTAGATTTTA
* * *
41494304 AAAATAAAAAATATATATTTTAATCATTTTAAAG-GAAAGTTTAAA-ATTTTAAAACAAAGTTTT
1 AAAATAAAAAATATAT-TTCTAATCATTTTAAAGAAAAAGTTTAAATATTTTAAAACAAAGTTCT
* *
41494367 GACTTTTCTCAACTATTTCAAAATAAAATTTTGAAATTTAAGAAAA-TAGTGTTTTTTTTAAAGA
65 GACTTTTCTCAACTATTTCAAAATAAAATTTTGAAATTTAAGAAAAGTAGTGATTTTTTAAAAGA
41494431 GAAAGTTT
130 GAAAGTTT
* * *
41494439 AAAATAAAAAATATGTTTCTAGTCATTTTAAAGAAAAAGTTTAAATTTTTTAAAACAAAGTTCTG
1 AAAATAAAAAATATATTTCTAATCATTTTAAAGAAAAAGTTTAAATATTTTAAAACAAAGTTCTG
* * * * * **
41494504 ATTTTTTTCAACTATTTCGATATAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTTTTAAAAGA
66 ACTTTTCTCAACTATTTCAAAATAAAATTTTGAAATTTAAGAAAAGTAGTGATTTTTTAAAAGA
41494568 AAATTTTGAT
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 15 0.14
135 25 0.23
136 55 0.50
137 16 0.14
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (137 bp):
AAAATAAAAAATATATTTCTAATCATTTTAAAGAAAAAGTTTAAATATTTTAAAACAAAGTTCTG
ACTTTTCTCAACTATTTCAAAATAAAATTTTGAAATTTAAGAAAAGTAGTGATTTTTTAAAAGAG
AAAGTTT
Found at i:41494549 original size:19 final size:20
Alignment explanation
Indices: 41494527--41494580 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
41494517 ATTTCGATAT
41494527 AAAGTTTTGATTTTT-AAGA
1 AAAGTTTTGATTTTTAAAGA
**
41494546 AAAGTAGTGATTTTTTAAAAGA
1 AAAGTTTTGA-TTTTT-AAAGA
41494568 AAA-TTTTGATTTT
1 AAAGTTTTGATTTT
41494581 GCAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 8 0.29
20 9 0.32
21 4 0.14
22 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (20 bp):
AAAGTTTTGATTTTTAAAGA
Found at i:41500356 original size:5 final size:5
Alignment explanation
Indices: 41500346--41500373 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41500336 AATTATAAAA
41500346 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
41500374 TATGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:41512863 original size:13 final size:13
Alignment explanation
Indices: 41512845--41512872 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41512835 TACCACATTT
41512845 ATATCATCAAAAC
1 ATATCATCAAAAC
41512858 ATATCATCAAAAC
1 ATATCATCAAAAC
41512871 AT
1 AT
41512873 TATTCAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (13 bp):
ATATCATCAAAAC
Found at i:41513642 original size:40 final size:41
Alignment explanation
Indices: 41513598--41513683 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
41513588 CACCTATTGC
* *
41513598 CTCATCGGAT-AATTCGAAGTAATAAATTGACACCCAGTGT
1 CTCATCGAATAAATCCGAAGTAATAAATTGACACCCAGTGT
41513638 CTCATCGAATAAATCCGAAGTAATAAATTGACACCCAGTGT
1 CTCATCGAATAAATCCGAAGTAATAAATTGACACCCAGTGT
41513679 CTCAT
1 CTCAT
41513684 TGGTTAAACC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (41 bp):
CTCATCGAATAAATCCGAAGTAATAAATTGACACCCAGTGT
Found at i:41513862 original size:25 final size:25
Alignment explanation
Indices: 41513834--41513892 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
41513824 AATACAACCA
*
41513834 ATATCCAATT-ATCATATTTACACAT
1 ATAT-CAATTCATAATATTTACACAT
*
41513859 ATAT--ATTCATAATATTTATACAT
1 ATATCAATTCATAATATTTACACAT
41513882 ATATCAATTCA
1 ATATCAATTCA
41513893 ATATCAAGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 3 0.10
23 17 0.59
25 9 0.31
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATCAATTCATAATATTTACACAT
Found at i:41514675 original size:29 final size:28
Alignment explanation
Indices: 41514616--41514675 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
41514606 AAGTAAAAAA
** *
41514616 TATTATAATATATATTTTAACTTTAATT
1 TATTATAATATATATAATAACTTTAACT
41514644 TATTAATAATATATATAATAA-TTTACACT
1 TATT-ATAATATATATAATAACTTTA-ACT
41514673 TAT
1 TAT
41514676 GCCACCTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTATAATATATATAATAACTTTAACT
Found at i:41524919 original size:21 final size:21
Alignment explanation
Indices: 41524893--41524977 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
41524883 TGCTCATAAA
*
41524893 TTTTGGTACATCCTCATATTT
1 TTTTGGTACTTCCTCATATTT
*
41524914 TTTTGGTACTTTCTCA-ATTT
1 TTTTGGTACTTCCTCATATTT
* *
41524934 TTTTGATATTTCCTCATATTT
1 TTTTGGTACTTCCTCATATTT
** * *
41524955 TTTTTATATTTCTTCATATTT
1 TTTTGGTACTTCCTCATATTT
41524976 TT
1 TT
41524978 GGAGTAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.30
21 39 0.70
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (21 bp):
TTTTGGTACTTCCTCATATTT
Found at i:41525246 original size:19 final size:19
Alignment explanation
Indices: 41525204--41525293 Score: 76
Period size: 19 Copynumber: 4.6 Consensus size: 19
41525194 CCCCTCATGT
*
41525204 TTTTTGGTATTTCCTCTTA
1 TTTTTGGTATTTCCTCATA
* *
41525223 ATTTTGGTATTTCTTCATA
1 TTTTTGGTATTTCCTCATA
*
41525242 TTTTT-TTAATATTCCCTCATCA
1 TTTTTGGT-AT-TT-CCTCAT-A
*
41525264 TTTTTGGTATCT-CTCATA
1 TTTTTGGTATTTCCTCATA
41525282 TTTTTTGGTATT
1 -TTTTTGGTATT
41525294 CTCTCGGATT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
18 2 0.04
19 37 0.66
20 2 0.04
21 6 0.11
22 8 0.14
23 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (19 bp):
TTTTTGGTATTTCCTCATA
Found at i:41525247 original size:40 final size:39
Alignment explanation
Indices: 41525197--41525294 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
41525187 TTGACATCCC
* * * *
41525197 CTCATGTTTTTTGGTATTTCCTC-TTAATTTTGGTATTT
1 CTCATATTTTTTGGTATTCCCTCATCAATTTTGGTATCT
** *
41525235 CTTCATATTTTTTTAATATTCCCTCATCATTTTTGGTATCT
1 C-TCATA-TTTTTTGGTATTCCCTCATCAATTTTGGTATCT
41525276 CTCATATTTTTTGGTATTC
1 CTCATATTTTTTGGTATTC
41525295 TCTCGGATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
38 1 0.02
39 15 0.31
40 19 0.40
41 13 0.27
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.58
Consensus pattern (39 bp):
CTCATATTTTTTGGTATTCCCTCATCAATTTTGGTATCT
Found at i:41525774 original size:13 final size:13
Alignment explanation
Indices: 41525756--41525784 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41525746 AGAACACAGC
41525756 CTAAACTCTTTGT
1 CTAAACTCTTTGT
41525769 CTAAACTCTTTGT
1 CTAAACTCTTTGT
41525782 CTA
1 CTA
41525785 TAAATATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (13 bp):
CTAAACTCTTTGT
Found at i:41535801 original size:79 final size:80
Alignment explanation
Indices: 41535716--41535869 Score: 229
Period size: 80 Copynumber: 1.9 Consensus size: 80
41535706 AAAATAGCCC
* * ** * * *
41535716 TAACATAATTGTAGTTAAT-GGAAATTTATTTCATTTATTTCTTATATAAGAATGGAAATTCAAG
1 TAACATAATTGAAGTTAATAAGAAATCCATTTCATTCAATTCTTATACAAGAATGGAAATTCAAG
41535780 TTGTAGGAATGTATG
66 TTGTAGGAATGTATG
41535795 TAACATAATTGAAGTTAATAAGAAATCCATTTCATTCAATTCTTATACAAGAATGGAAATTCAAG
1 TAACATAATTGAAGTTAATAAGAAATCCATTTCATTCAATTCTTATACAAGAATGGAAATTCAAG
*
41535860 TTGTTGGAAT
66 TTGTAGGAAT
41535870 ATATAATAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 18 0.27
80 48 0.73
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (80 bp):
TAACATAATTGAAGTTAATAAGAAATCCATTTCATTCAATTCTTATACAAGAATGGAAATTCAAG
TTGTAGGAATGTATG
Found at i:41548712 original size:8 final size:8
Alignment explanation
Indices: 41548696--41548732 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
41548686 GCAGGCTTAT
41548696 AATTGGAA
1 AATTGGAA
*
41548704 AATTAGAA
1 AATTGGAA
41548712 AATTGGAA
1 AATTGGAA
41548720 AATTGGAA
1 AATTGGAA
41548728 AATTG
1 AATTG
41548733 ATGCAACTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (8 bp):
AATTGGAA
Found at i:41552907 original size:40 final size:40
Alignment explanation
Indices: 41552846--41552968 Score: 178
Period size: 40 Copynumber: 3.1 Consensus size: 40
41552836 CGCTCGGGCA
*
41552846 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-TG
**
41552886 AAAAACGCCGCTAAAGGTCAAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
* *
41552926 GAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
41552965 AAAA
1 AAAA
41552969 GCGACGCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 24 0.32
40 50 0.68
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:41553074 original size:41 final size:41
Alignment explanation
Indices: 41553016--41553095 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
41553006 TGGGTTTTTG
* *
41553016 GGGCCTTTAGCGACGTTTTTGAGGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAAGAAACGCCGCTAATGCTC
*
41553057 GGGCCTTTAGCGGCGTTTTTGAAGAAACGCCGCTAATGC
1 GGGCCTTTAGCGACGTTTTTGAAGAAACGCCGCTAATGC
41553096 CCGTTTTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (41 bp):
GGGCCTTTAGCGACGTTTTTGAAGAAACGCCGCTAATGCTC
Found at i:41553544 original size:14 final size:15
Alignment explanation
Indices: 41553518--41553546 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41553508 AATGTTTATA
41553518 GATTATGGGATTAGG
1 GATTATGGGATTAGG
41553533 GATTAT-GGATTAGG
1 GATTATGGGATTAGG
41553547 AATTTTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (15 bp):
GATTATGGGATTAGG
Found at i:41554245 original size:11 final size:12
Alignment explanation
Indices: 41554244--41554369 Score: 59
Period size: 11 Copynumber: 11.5 Consensus size: 12
41554234 TTTTAAAAAA
41554244 TTAAAAAAAGTATT
1 TTAA-AAAA-TATT
41554258 TT-AAAAATATT
1 TTAAAAAATATT
41554269 TT-AAAAATATT
1 TTAAAAAATATT
41554280 TT---AAA-A--
1 TTAAAAAATATT
*
41554286 TTAAAAAA-AAT
1 TTAAAAAATATT
*
41554297 TAAAAAAAGTATT
1 TTAAAAAA-TATT
41554310 TT-AAAAATATT
1 TTAAAAAATATT
41554321 TT---AAA-ATT
1 TTAAAAAATATT
*
41554329 TTAAAAAA-AAT
1 TTAAAAAATATT
*
41554340 TAAAAAAAGTA-T
1 TTAAAAAA-TATT
*
41554352 GTAAAAAATATT
1 TTAAAAAATATT
41554364 TTAAAA
1 TTAAAA
41554370 TTAAAAAAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.02
8 6 0.07
9 10 0.11
11 44 0.48
12 22 0.24
13 5 0.05
14 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:41554259 original size:22 final size:21
Alignment explanation
Indices: 41554229--41554380 Score: 95
Period size: 22 Copynumber: 7.3 Consensus size: 21
41554219 TTTTTATTTT
41554229 AAAAT-TTTTAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
**
41554249 AAAAGTATTTTAAAAATATTTTA
1 AAAA-TATTTTAAAAA-ATTAAA
41554272 AAAATATTTT--AAAATTAAA
1 AAAATATTTTAAAAAATTAAA
** **
41554291 AAAA-ATTAAAAAAAGTATTTTA
1 AAAATATTTTAAAAA--ATTAAA
**
41554313 AAAATATTTTAAAATTTTAAA
1 AAAATATTTTAAAAAATTAAA
* *
41554334 AAAA-A-TTAAAAAAAGTATGTAA
1 AAAATATTTTAAAAAA-T-T-AAA
41554356 AAAATATTTT--AAAATTAAA
1 AAAATATTTTAAAAAATTAAA
41554375 AAAATA
1 AAAATA
41554381 AATATATTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
18 3 0.03
19 22 0.22
20 13 0.13
21 10 0.10
22 33 0.33
23 16 0.16
24 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAATATTTTAAAAAATTAAA
Found at i:41554294 original size:43 final size:41
Alignment explanation
Indices: 41554223--41554378 Score: 201
Period size: 43 Copynumber: 3.7 Consensus size: 41
41554213 GGCCCATTTT
**
41554223 TATTTT-AAAAT-TTTTAAAAAATTAAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTTT--AAAATTAAAAAAA--ATTAAAAAAAG
41554265 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAG
41554306 TATTTTAAAAATATTTTAAAATTTTAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAA--TTAAAAAAAATTAAAAAAAG
* *
41554349 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAA
41554379 TAAATATATT
Statistics
Matches: 105, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
40 8 0.08
41 30 0.29
42 19 0.18
43 44 0.42
44 4 0.04
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (41 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAG
Found at i:41554301 original size:9 final size:10
Alignment explanation
Indices: 41554282--41554347 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
41554272 AAAATATTTT
41554282 AAAATTAAAA
1 AAAATTAAAA
41554292 AAAATTAAAA
1 AAAATTAAAA
*
41554302 AAAGTATTTTAAA
1 AAA--A-TTAAAA
* **
41554315 AATATTTTAA
1 AAAATTAAAA
**
41554325 AATTTTAAAA
1 AAAATTAAAA
41554335 AAAATTAAAA
1 AAAATTAAAA
41554345 AAA
1 AAA
41554348 GTATGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 36 0.80
11 1 0.02
12 1 0.02
13 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:41554312 original size:52 final size:53
Alignment explanation
Indices: 41554223--41554326 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
41554213 GGCCCATTTT
**
41554223 TATTTTAAAATTTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAATTTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
41554276 TATTTTAAAA-TTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TATTTTAAAATTTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
41554327 TTTTAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 39 0.80
53 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (53 bp):
TATTTTAAAATTTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:41554345 original size:19 final size:19
Alignment explanation
Indices: 41554307--41554345 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41554297 TAAAAAAAGT
* * *
41554307 ATTTTAAAAATATTTTAAA
1 ATTTTAAAAAAAATTAAAA
41554326 ATTTTAAAAAAAATTAAAA
1 ATTTTAAAAAAAATTAAAA
41554345 A
1 A
41554346 AAGTATGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTTAAAAAAAATTAAAA
Done.