Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold962
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: 160331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:7012 original size:26 final size:26
Alignment explanation
Indices: 6982--7067 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
6972 AAGTTGGTGG
6982 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
* * * * **
7008 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCTCA-AAG-AGCAGGA
7037 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
7063 CACCT
1 CACCT
7068 CTTAAAGCCC
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 8 0.19
28 8 0.19
29 8 0.19
30 3 0.07
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCTCAAAGAGCAGGA
Found at i:7019 original size:55 final size:55
Alignment explanation
Indices: 6935--7565 Score: 924
Period size: 55 Copynumber: 11.3 Consensus size: 55
6925 TCCGCTTTTT
6935 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
6990 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7045 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
7100 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
7155 AGTCCTCAAAGAGCAGGACATCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
7211 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
7267 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* **
7322 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*** * *
7377 AGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
7438 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** * *
7493 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
7548 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
7566 TACACTTTAT
Statistics
Matches: 524, Mismatches: 41, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
54 5 0.01
55 359 0.69
56 113 0.22
57 1 0.00
59 1 0.00
60 3 0.01
61 42 0.08
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:7460 original size:26 final size:26
Alignment explanation
Indices: 7430--7517 Score: 63
Period size: 26 Copynumber: 3.3 Consensus size: 26
7420 AAGTTGGTGG
7430 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
7456 CACCTCTTAAAG-CCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCC-CA-AAG-AGCAGGA
*
7485 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
*
7511 CGCCTTT
1 CACCTTT
7518 TAAAGCCCAC
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 3 0.07
26 14 0.31
27 9 0.20
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:8353 original size:21 final size:20
Alignment explanation
Indices: 8327--8396 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
8317 AATTCCAAAT
*
8327 TCGATACATTTGTAGAATGTA
1 TCGATACATTTATA-AATGTA
* *
8348 TCGATACATTCACAAATGTA
1 TCGATACATTTATAAATGTA
*
8368 TCGATACATTCTACAAATGTA
1 TCGATACATT-TATAAATGTA
8389 TCGATACA
1 TCGATACA
8397 GGGTCCCAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
TCGATACATTTATAAATGTA
Found at i:8367 original size:20 final size:21
Alignment explanation
Indices: 8342--8396 Score: 103
Period size: 20 Copynumber: 2.7 Consensus size: 21
8332 ACATTTGTAG
8342 AATGTATCGATACATTC-ACA
1 AATGTATCGATACATTCTACA
8362 AATGTATCGATACATTCTACA
1 AATGTATCGATACATTCTACA
8383 AATGTATCGATACA
1 AATGTATCGATACA
8397 GGGTCCCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACATTCTACA
Found at i:8456 original size:19 final size:19
Alignment explanation
Indices: 8432--8499 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
8422 AATTCAACGA
8432 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
8451 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
8466 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
8483 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
8500 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:8470 original size:32 final size:32
Alignment explanation
Indices: 8434--8496 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
8424 TTCAACGATT
*
8434 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
8466 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
8497 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:8471 original size:13 final size:13
Alignment explanation
Indices: 8453--8477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8443 ACATAAGTTT
8453 TGTATCGATACAA
1 TGTATCGATACAA
8466 TGTATCGATACA
1 TGTATCGATACA
8478 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8557 original size:13 final size:13
Alignment explanation
Indices: 8539--8564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8529 CATTTTTCTG
8539 TGTATCGATACAT
1 TGTATCGATACAT
8552 TGTATCGATACAT
1 TGTATCGATACAT
8565 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8561 original size:33 final size:33
Alignment explanation
Indices: 8519--8585 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8509 GCCAAGGAAA
***
8519 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
8552 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
8585 T
1 T
8586 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:11059 original size:55 final size:51
Alignment explanation
Indices: 10927--11270 Score: 151
Period size: 51 Copynumber: 6.5 Consensus size: 51
10917 TTGAGTTTAT
* * * * *
10927 CAATTCTCCACAATCGAGGATATTCCAACTCTGATTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* *
10978 TAATT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAACAC
* * * * ** * *
11032 CAATTTCTTCACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACAC
* ** * * * * *
11085 CAATCCCGTT-A-TTTCTGAGGGGATACTCCAACCCCGACTTTATTTTCAAAATAT
1 CAAT-TC-TTCACAATC---GGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * * * * * *
11139 CGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* ** * * *
11190 CAATTTCTCCTTTAATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATAT
1 CAA-TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* *
11244 CGATT-TCTCACAACCGGGGATACTCCA
1 CAATTCT-TCACAATCGGGGATACTCCA
11271 GCCCCGTTAT
Statistics
Matches: 215, Mismatches: 56, Indels: 43
0.68 0.18 0.14
Matches are distributed among these distances:
50 2 0.01
51 67 0.31
52 25 0.12
53 47 0.22
54 26 0.12
55 40 0.19
56 4 0.02
57 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:11165 original size:51 final size:51
Alignment explanation
Indices: 11103--11276 Score: 186
Period size: 51 Copynumber: 3.4 Consensus size: 51
11093 TTATTTCTGA
*
11103 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATATCGATTTTTCATAATC
* * * * * * *
11154 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATATCGATTT-TTC-ATAATC
** * * * *
11207 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATATCGATTTCTCACAACC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATATCGATTTTTCATAATC
*
11259 GGGGATACTCCAGCCCCG
1 GGGGATACTCCAACCCCG
11277 TTATTTTCAA
Statistics
Matches: 96, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
51 36 0.38
52 20 0.21
53 31 0.32
54 9 0.09
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATATCGATTTTTCATAATC
Found at i:11294 original size:105 final size:101
Alignment explanation
Indices: 10988--11294 Score: 278
Period size: 105 Copynumber: 2.9 Consensus size: 101
10978 TAATTTTCTA
* * *
10988 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAAATATCGATTTC-TCACAATCGGGGA
* ** * *
11053 CACTCCAACCCCGTTAATCATCGGGGATACTCCAATCCCGT
63 TACTCCAACCCCGTT-ATTTTCAGGGA-ACACCAATCCCGT
* * * * * *
11094 TATTTCTGAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTTCATAATCGGGG
1 TA-ATC---GGGGATACTCCAACTCCGATTTTATTTCCAAAAATATCGATTTCTCACAATCGGGG
* *
11158 ATACTCCAACCCCGGTTTTATTTTCA--CAACACCAATTTCTCCTT
62 ATACTCCAACCCC-G--TTATTTTCAGGGAACACCAA--TC-CCGT
* *
11202 TAATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATATCGATTTCTCACAACCGGGGATAC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATATCGATTTCTCACAATCGGGGATAC
*
11267 TCCAGCCCCGTTATTTTCAAGGGAACAC
66 TCCAACCCCGTTATTTTC-AGGGAACAC
11295 TCCAACCCTG
Statistics
Matches: 161, Mismatches: 26, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
102 8 0.05
103 1 0.01
104 26 0.16
105 46 0.29
106 26 0.16
107 17 0.11
108 9 0.06
109 2 0.01
110 26 0.16
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (101 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATATCGATTTCTCACAATCGGGGATAC
TCCAACCCCGTTATTTTCAGGGAACACCAATCCCGT
Found at i:13847 original size:20 final size:20
Alignment explanation
Indices: 13768--13847 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
13758 AATGTCCAAA
*
13768 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
13788 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
13813 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
13833 TTGTATCGATACATT
1 ATGTATCGATACATT
13848 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:13872 original size:13 final size:13
Alignment explanation
Indices: 13834--13872 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
13824 CATTTTTCTT
*
13834 TGTATCGATACAT
1 TGTATCGATACAG
13847 TGTATCGATACAG
1 TGTATCGATACAG
13860 TGTATCGATACAG
1 TGTATCGATACAG
13873 GGTGATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:14035 original size:20 final size:20
Alignment explanation
Indices: 13992--14037 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
13982 AAATCTTTTG
13992 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
14013 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
14033 CAAAA
1 CAAAA
14038 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:16430 original size:13 final size:13
Alignment explanation
Indices: 16412--16437 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16402 TACAGCAAGT
16412 ATGTATCGATACA
1 ATGTATCGATACA
16425 ATGTATCGATACA
1 ATGTATCGATACA
16438 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:19121 original size:52 final size:51
Alignment explanation
Indices: 19064--19180 Score: 155
Period size: 52 Copynumber: 2.3 Consensus size: 51
19054 AAATTTGCCT
* *
19064 GAATGTATCCATATAATAAAGAATGTATCAATACATTTGGGTCAAAAACCAA
1 GAATGTATCCATACAATAAAGAATATATCAATACATTTGGGT-AAAAACCAA
* * * *
19116 GAATGTATCGATACAGTAAAGAATATATTAATACATTTGGGTTAAAACCAA
1 GAATGTATCCATACAATAAAGAATATATCAATACATTTGGGTAAAAACCAA
*
19167 -AATGTATCGATACA
1 GAATGTATCCATACA
19181 TTTCCATTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 14 0.24
51 8 0.14
52 37 0.63
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (51 bp):
GAATGTATCCATACAATAAAGAATATATCAATACATTTGGGTAAAAACCAA
Found at i:24094 original size:3 final size:3
Alignment explanation
Indices: 24088--24126 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
24078 ATCATCATGA
*
24088 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24127 TATTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24131 original size:3 final size:3
Alignment explanation
Indices: 24125--24166 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
24115 AATAATAATA
*
24125 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24167 TAAGAAAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25165 original size:19 final size:20
Alignment explanation
Indices: 25116--25169 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
25106 AATTAAATTA
*
25116 TTATACAATTTTTATTTTGT
1 TTATAAAATTTTTATTTTGT
* *
25136 TT-TAGATTTTTTATTTT-T
1 TTATAAAATTTTTATTTTGT
25154 TTATAAAA-TTTTATTT
1 TTATAAAATTTTTATTT
25170 CAATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.38
19 16 0.55
20 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TTATAAAATTTTTATTTTGT
Found at i:25478 original size:90 final size:90
Alignment explanation
Indices: 25325--25504 Score: 324
Period size: 90 Copynumber: 2.0 Consensus size: 90
25315 TATTGATGAA
*
25325 ACCCAACCGATATTTTTATTTATGTCCTGTCCTATGTCTCATATGGGATAGAGGGAAATTGCCCA
1 ACCCAACCGATATTTTTATTTATGTCCTGTCCTATGTCTCATATGAGATAGAGGGAAATTGCCCA
25390 TTCAATATTGAAGTCAGAGAGAAGT
66 TTCAATATTGAAGTCAGAGAGAAGT
* * *
25415 ACCCAACCGATATTTTTATTTATGTCCTGTCCTATGTCTCATTTGATATTGAGGGAAATTGCCCA
1 ACCCAACCGATATTTTTATTTATGTCCTGTCCTATGTCTCATATGAGATAGAGGGAAATTGCCCA
25480 TTCAATATTGAAGTCAGAGAGAAGT
66 TTCAATATTGAAGTCAGAGAGAAGT
25505 GTAGGGACGT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (90 bp):
ACCCAACCGATATTTTTATTTATGTCCTGTCCTATGTCTCATATGAGATAGAGGGAAATTGCCCA
TTCAATATTGAAGTCAGAGAGAAGT
Found at i:26456 original size:14 final size:14
Alignment explanation
Indices: 26432--26464 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
26422 CAAGGATGAG
26432 CAAGA-TAAGAAAA
1 CAAGAGTAAGAAAA
26445 CAAGAGTAAGAAAA
1 CAAGAGTAAGAAAA
*
26459 AAAGAG
1 CAAGAG
26465 GAGATAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.67, C:0.06, G:0.21, T:0.06
Consensus pattern (14 bp):
CAAGAGTAAGAAAA
Found at i:27732 original size:19 final size:20
Alignment explanation
Indices: 27699--27752 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
27689 TAAAATATTT
*
27699 TAAATATAATT-ATAATAATA
1 TAAATAT-ATTAATAATAACA
27719 -AAATATATTAATAA-AACA
1 TAAATATATTAATAATAACA
*
27737 TAAATATATGAATAAT
1 TAAATATATTAATAAT
27753 CAGAGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAATATATTAATAATAACA
Found at i:30019 original size:2 final size:2
Alignment explanation
Indices: 30012--30046 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30002 AGTTCTTGTC
30012 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
30047 ATCCGTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:32594 original size:14 final size:14
Alignment explanation
Indices: 32575--32604 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
32565 GTCTTGATGC
32575 TATATATATGTATA
1 TATATATATGTATA
32589 TATATATATGTATA
1 TATATATATGTATA
32603 TA
1 TA
32605 GATACATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATATATATGTATA
Found at i:33201 original size:49 final size:54
Alignment explanation
Indices: 33116--33242 Score: 133
Period size: 52 Copynumber: 2.4 Consensus size: 54
33106 ATTTGGTAGT
* *
33116 TTATATATTTATATGATATATTTTAATGTGTTAATAA-TAATATTTTA-AAATA
1 TTATATATTTATATGATATATTTTAATATGTGAATAATTAATATTTTATAAATA
* * *
33168 TTATGTATTTATAT-A-A-ATTTTAATATGTGAATAATTTATATTTTATAAATT
1 TTATATATTTATATGATATATTTTAATATGTGAATAATTAATATTTTATAAATA
*
33219 TTGATAT-TTTA-ATGTATTTATTTT
1 TT-ATATATTTATATG-ATATATTTT
33243 TTATGTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
49 16 0.26
50 12 0.20
51 11 0.18
52 17 0.28
54 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (54 bp):
TTATATATTTATATGATATATTTTAATATGTGAATAATTAATATTTTATAAATA
Found at i:33227 original size:17 final size:16
Alignment explanation
Indices: 33155--33230 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 16
33145 GTTAATAATA
33155 ATATTTTAAAATATTATG
1 ATATTTTAAAAT-TT-TG
*
33173 -TATTTATATAAATTTTA
1 ATATTT-TA-AAATTTTG
* *
33190 ATATGTGAATAA-TTT-
1 ATATTTTAA-AATTTTG
33205 ATATTTTATAAATTTTG
1 ATATTTTA-AAATTTTG
33222 ATATTTTAA
1 ATATTTTAA
33231 TGTATTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
15 8 0.17
16 9 0.20
17 17 0.37
18 8 0.17
19 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATATTTTAAAATTTTG
Found at i:33238 original size:33 final size:32
Alignment explanation
Indices: 33153--33246 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
33143 GTGTTAATAA
* *
33153 TAATATTTTAAAATATTATGTATTTATATAAATTT
1 TAATATTTT-AATTATT-TATATTT-TATAAATTT
* * *
33188 TAATATGTGAATAATTTATATTTTATAAATTT
1 TAATATTTTAATTATTTATATTTTATAAATTT
* *
33220 TGATATTTTAATGTATTTATTTTTTAT
1 TAATATTTTAAT-TATTTATATTTTAT
33247 GTATTATATT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
32 18 0.38
33 18 0.38
34 5 0.10
35 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.57
Consensus pattern (32 bp):
TAATATTTTAATTATTTATATTTTATAAATTT
Found at i:33248 original size:15 final size:16
Alignment explanation
Indices: 33225--33265 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
33215 AATTTTGATA
*
33225 TTTTAATGTATT-TAT
1 TTTTTATGTATTATAT
33240 TTTTTATGTATTATAT
1 TTTTTATGTATTATAT
*
33256 TTATTATGTA
1 TTTTTATGTA
33266 ATTGTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (16 bp):
TTTTTATGTATTATAT
Found at i:33330 original size:15 final size:13
Alignment explanation
Indices: 33297--33327 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33287 TTAATTTTAA
33297 ATATAATATAATT
1 ATATAATATAATT
*
33310 ATATAATATAAAT
1 ATATAATATAATT
33323 ATATA
1 ATATA
33328 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:33343 original size:10 final size:10
Alignment explanation
Indices: 33295--33373 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 10
33285 TATTAATTTT
33295 AAATATAATA
1 AAATATAATA
33305 TAATTATATAATA
1 -AA--ATATAATA
33318 TAAATATATATA
1 -AAATATA-ATA
*
33330 AAAAATAATTA
1 AAATATAA-TA
33341 AAATATAATA
1 AAATATAATA
33351 AAATTATAA-A
1 AAA-TATAATA
*
33361 AAACATAA-A
1 AAATATAATA
33370 AAAT
1 AAAT
33374 CACATACGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
9 8 0.14
10 10 0.17
11 27 0.46
12 3 0.05
13 11 0.19
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATATAATA
Found at i:33360 original size:18 final size:18
Alignment explanation
Indices: 33325--33373 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
33315 ATATAAATAT
33325 ATATAAAAAATAATTAAA
1 ATATAAAAAATAATTAAA
* *
33343 ATATAATAAAATTATAAAAA
1 ATATAA-AAAATAAT-TAAA
*
33363 ACATAAAAAAT
1 ATATAAAAAAT
33374 CACATACGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
ATATAAAAAATAATTAAA
Found at i:36708 original size:20 final size:19
Alignment explanation
Indices: 36659--36708 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
36649 GATATAATTT
* *
36659 TTTAAATACTCTTAAAATA
1 TTTAAATAATCTTAAAAAA
*
36678 -TTAAAAAATCTTAAAAAA
1 TTTAAATAATCTTAAAAAA
36696 TTTAAATATATCT
1 TTTAAATA-ATCT
36709 ATATTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 15 0.60
19 6 0.24
20 4 0.16
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTAAATAATCTTAAAAAA
Found at i:39512 original size:21 final size:21
Alignment explanation
Indices: 39488--39533 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39478 TGAGTCTAGG
* *
39488 ATATTTTTAAATCCTGGATAA
1 ATATATTTAAATACTGGATAA
*
39509 ATATATTTAAATACTTGATAA
1 ATATATTTAAATACTGGATAA
39530 ATAT
1 ATAT
39534 GATTGCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
ATATATTTAAATACTGGATAA
Found at i:41507 original size:18 final size:16
Alignment explanation
Indices: 41484--41538 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 16
41474 AAATTTAAAA
41484 TATAAATATAAAAATATT
1 TATAAAT-TAAAAAT-TT
41502 TATAAATTAAATTAATTT
1 TATAAATTAAA--AATTT
*
41520 TTTAAATTTAAAAATTT
1 TATAAA-TTAAAAATTT
41537 TA
1 TA
41539 ATTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 10 0.31
18 14 0.44
19 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATTAAAAATTT
Found at i:41598 original size:18 final size:17
Alignment explanation
Indices: 41576--41627 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
41566 CATATTAAGT
41576 TAAAAAATAAATTTAAA
1 TAAAAAATAAATTTAAA
41593 TAAAAATATAATTATTT--A
1 TAAAAA-ATAA--ATTTAAA
41611 TAAAAAATAAA-TTAAA
1 TAAAAAATAAATTTAAA
41627 T
1 T
41628 TTTAATTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
14 2 0.07
15 1 0.03
16 2 0.07
17 10 0.33
18 11 0.37
20 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAATAAATTTAAA
Found at i:41743 original size:21 final size:21
Alignment explanation
Indices: 41719--41758 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41709 AATTTTTATC
41719 ATATAATAATAAAAATATATA
1 ATATAATAATAAAAATATATA
* **
41740 ATATTATAATTTAAATATA
1 ATATAATAATAAAAATATA
41759 AAAATTATTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAATAATAAAAATATATA
Found at i:41792 original size:17 final size:17
Alignment explanation
Indices: 41752--41788 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
41742 ATTATAATTT
41752 AAATATAAAAATTATTAA
1 AAAT-TAAAAATTATTAA
41770 AAATTAAAAATT-TTAA
1 AAATTAAAAATTATTAA
41786 AAA
1 AAA
41789 ATTATTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTAAAAATTATTAA
Found at i:42901 original size:2 final size:2
Alignment explanation
Indices: 42896--42920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42886 AATATATCTG
42896 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
42921 GGAGGGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43485 original size:5 final size:5
Alignment explanation
Indices: 43475--43502 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43465 AGATTCGAAA
43475 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
43503 GAGGAGTAGT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:45047 original size:6 final size:6
Alignment explanation
Indices: 45036--45064 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
45026 CCCTGCATGC
45036 ATGTCA ATGTCA ATGTCA ATGTCA ATGTC
1 ATGTCA ATGTCA ATGTCA ATGTCA ATGTC
45065 CATGCCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
ATGTCA
Found at i:46173 original size:23 final size:24
Alignment explanation
Indices: 46147--46196 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
46137 TAATATATAT
*
46147 TTAAAATAAATAA-AATAAAATAA
1 TTAAAATAAATAATAATAAAAAAA
46170 TT-AAATAAATAATAATAAAAAAA
1 TTAAAATAAATAATAATAAAAAAA
46193 TTAA
1 TTAA
46197 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 13 0.54
24 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
TTAAAATAAATAATAATAAAAAAA
Found at i:46176 original size:18 final size:18
Alignment explanation
Indices: 46153--46187 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46143 ATATTTAAAA
46153 TAAATAAAATAA-AATAAT
1 TAAAT-AAATAATAATAAT
46171 TAAATAAATAATAATAA
1 TAAATAAATAATAATAA
46188 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATAAATAATAATAAT
Found at i:46342 original size:13 final size:13
Alignment explanation
Indices: 46324--46348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46314 AACCACTTTA
46324 TTATTAATAATAT
1 TTATTAATAATAT
46337 TTATTAATAATA
1 TTATTAATAATA
46349 ACACCACGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATTAATAATAT
Found at i:48745 original size:31 final size:31
Alignment explanation
Indices: 48707--48775 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
48697 TGTTATTTAG
*
48707 ATATTTTTCATATCAAACTTATTGGTCAACC
1 ATATTTTTCATATCAAACTTATTAGTCAACC
48738 ATATTTTTCATATCAAACTTATTAGTCAACC
1 ATATTTTTCATATCAAACTTATTAGTCAACC
48769 ATGATTT
1 AT-ATTT
48776 GGTAGCACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.43
Consensus pattern (31 bp):
ATATTTTTCATATCAAACTTATTAGTCAACC
Found at i:51938 original size:15 final size:15
Alignment explanation
Indices: 51920--51967 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
51910 AAATATTGAT
*
51920 TATACAATATATTTA
1 TATAAAATATATTTA
** *
51935 TATATTATATATCTA
1 TATAAAATATATTTA
51950 TATAAAATA-ATTTA
1 TATAAAATATATTTA
51964 TATA
1 TATA
51968 TTAATACATA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAAAATATATTTA
Found at i:51986 original size:17 final size:18
Alignment explanation
Indices: 51959--51994 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
51949 ATATAAAATA
51959 ATTTATATATTAATACAT
1 ATTTATATATTAATACAT
*
51977 ATTT-TATATTTATACAT
1 ATTTATATATTAATACAT
51994 A
1 A
51995 AATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATATATTAATACAT
Found at i:55466 original size:15 final size:15
Alignment explanation
Indices: 55446--55475 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55436 GGTTATATTG
55446 AGACTAAGCTATCTT
1 AGACTAAGCTATCTT
55461 AGACTAAGCTATCTT
1 AGACTAAGCTATCTT
55476 GCAGTTTTGT
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:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
AGACTAAGCTATCTT
Found at i:55800 original size:3 final size:3
Alignment explanation
Indices: 55792--55816 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55782 CCTAAGGAAG
55792 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
55817 GTTAATTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:57368 original size:20 final size:19
Alignment explanation
Indices: 57336--57373 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
57326 TATAACATAA
57336 AATTGAAAGTTATTAATTTC
1 AATTGAAAGTTA-TAATTTC
57356 AATT-AAAGTTTATAATTT
1 AATTGAAAG-TTATAATTT
57374 TAAGCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (19 bp):
AATTGAAAGTTATAATTTC
Found at i:57973 original size:36 final size:34
Alignment explanation
Indices: 57902--57973 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
57892 AGAATAGATA
*
57902 AATATATAAAAATTTATAAAAATAATAAATTTTT
1 AATATATAAAAATTTATAAAAATAATAAATCTTT
*
57936 AATATATCAAAATTTATATAAAAT-ATATAATACTTT
1 AATATATAAAAATTTATA-AAAATAATA-AAT-CTTT
57972 AA
1 AA
57974 ATACGATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 20 0.61
35 8 0.24
36 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (34 bp):
AATATATAAAAATTTATAAAAATAATAAATCTTT
Found at i:59144 original size:20 final size:20
Alignment explanation
Indices: 59119--59162 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
59109 AGGTGTAAGT
* *
59119 ATATTATAATTTAAGGGACG
1 ATATTATAATCTAAAGGACG
*
59139 ATATTATAATCTAAAGGATG
1 ATATTATAATCTAAAGGACG
59159 ATAT
1 ATAT
59163 ATGAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (20 bp):
ATATTATAATCTAAAGGACG
Found at i:59746 original size:118 final size:120
Alignment explanation
Indices: 59624--59973 Score: 349
Period size: 119 Copynumber: 3.0 Consensus size: 120
59614 GATTTTGTAA
* * * *
59624 TAAATTTTACTAATATTTATAATACAAAATCATAAAT-AAGAGTGAAATATAT-TTGATTACTTC
1 TAAATTTTACTAATATTTATAATACAAAATAAGAAATAAAGAATGAAATAAATCTT-ATTACTTC
* *
59687 TTATAATATATTATAAAATATTTATATTA-AGAAAAATC-TATTTATTAATAAAATT
65 TTATAATATAATATAAAATATTTATATTATA-AAAAAACATATTTATTAATAAAATT
* * *
59742 TAAATTTTATTAGTATTTATAGTACAAAATAAGAAATAAAGAATGAAATAAATCTTATTACTTCT
1 TAAATTTTACTAATATTTATAATACAAAATAAGAAATAAAGAATGAAATAAATCTTATTACTTCT
*
59807 TATAATATAATATAAACTATTTATATTATAAAAAAACATATTTATT--T---A--
66 TATAATATAATATAAAATATTTATATTATAAAAAAACATATTTATTAATAAAATT
* *
59855 TAAA-ATT--TAA-ATTTATAATACAAAATAA-AAGA-AAAGAATGAAATAATTCTTATTACTTC
1 TAAATTTTACTAATATTTATAATACAAAATAAGAA-ATAAAGAATGAAATAAATCTTATTACTTC
* * * * * *
59914 TTATATATAATACAACATAAAATATCTATACTA-GAAAAAACCTATTTATTTATAAAATT
65 TTATA-AT-AT--AATATAAAATATTTATATTATAAAAAAACATATTTATTAATAAAATT
59973 T
1 T
59974 TACATATTGA
Statistics
Matches: 196, Mismatches: 20, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
108 33 0.17
109 20 0.10
110 4 0.02
111 15 0.08
112 18 0.09
113 5 0.03
115 1 0.01
116 1 0.01
118 34 0.17
119 54 0.28
120 11 0.06
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (120 bp):
TAAATTTTACTAATATTTATAATACAAAATAAGAAATAAAGAATGAAATAAATCTTATTACTTCT
TATAATATAATATAAAATATTTATATTATAAAAAAACATATTTATTAATAAAATT
Found at i:59859 original size:19 final size:20
Alignment explanation
Indices: 59806--59859 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
59796 TTATTACTTC
* *
59806 TTATAATATAATATAAACTAT
1 TTATATTATAA-AAAAACTAT
59827 TTATATTATAAAAAAACATAT
1 TTATATTATAAAAAAAC-TAT
59848 TTAT-TTATAAAA
1 TTATATTATAAAA
59860 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATATTATAAAAAAACTAT
Found at i:60581 original size:21 final size:22
Alignment explanation
Indices: 60544--60584 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
60534 ATATTTTATT
*
60544 TAAATTTTAATTATAAAATATA
1 TAAATATTAATTATAAAATATA
60566 TAAATATTAA-TATAAAATA
1 TAAATATTAATTATAAAATA
60585 AATTTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATTAATTATAAAATATA
Found at i:62354 original size:2 final size:2
Alignment explanation
Indices: 62347--62383 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
62337 TCTTCGCTGC
62347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62384 CATGTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62979 original size:20 final size:21
Alignment explanation
Indices: 62934--62980 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
62924 ATATTTTCAA
*
62934 TATAAAAATAATATGAAAATG
1 TATAAAAATAAGATGAAAATG
*
62955 T-TAAAAATAAGAT-AAATTG
1 TATAAAAATAAGATGAAAATG
62974 TATAAAA
1 TATAAAA
62981 TTAAATTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
TATAAAAATAAGATGAAAATG
Found at i:65970 original size:2 final size:2
Alignment explanation
Indices: 65963--65993 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
65953 ATTGCATTAC
*
65963 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65994 GACATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:67806 original size:15 final size:14
Alignment explanation
Indices: 67786--67831 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
67776 TCTATAAGGG
67786 GACATAAAATGTGAA
1 GACATAAAA-GTGAA
*
67801 GACATAATAAGTGAG
1 GACATAA-AAGTGAA
67816 GACATGAAAAGTGAA
1 GACAT-AAAAGTGAA
67831 G
1 G
67832 CTTTTGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (14 bp):
GACATAAAAGTGAA
Found at i:68654 original size:6 final size:6
Alignment explanation
Indices: 68626--68675 Score: 66
Period size: 6 Copynumber: 8.3 Consensus size: 6
68616 AAAATAATAA
* *
68626 AATATA AATATT ATTGATT -ATATT AATATT AATATT AATATT AATATT
1 AATATT AATATT AAT-ATT AATATT AATATT AATATT AATATT AATATT
68674 AA
1 AA
68676 GTATATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
5 3 0.08
6 33 0.85
7 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:68849 original size:14 final size:14
Alignment explanation
Indices: 68830--68859 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
68820 TATTTAATTT
*
68830 AATAAATAAATATA
1 AATAAATAAAAATA
68844 AATAAATAAAAATA
1 AATAAATAAAAATA
68858 AA
1 AA
68860 AATTATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:69585 original size:3 final size:3
Alignment explanation
Indices: 69579--69618 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
69569 AACAATAATA
69579 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
69619 TTGACTTTTA
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:70082 original size:17 final size:17
Alignment explanation
Indices: 70056--70089 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
70046 ATAAATCGGT
70056 CCAGAAGACCTTTGTTA
1 CCAGAAGACCTTTGTTA
*
70073 CCAGATGACCTTTGTTA
1 CCAGAAGACCTTTGTTA
70090 AGGTTTCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
CCAGAAGACCTTTGTTA
Found at i:72553 original size:13 final size:13
Alignment explanation
Indices: 72535--72564 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
72525 ATGACAAAGA
72535 AAGCATGTGAAGC
1 AAGCATGTGAAGC
72548 AAGCATGTGAAGC
1 AAGCATGTGAAGC
72561 AAGC
1 AAGC
72565 TTGACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (13 bp):
AAGCATGTGAAGC
Found at i:73478 original size:18 final size:17
Alignment explanation
Indices: 73450--73484 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
73440 GATGATCAAT
73450 TTAAACCTTTGGGAAAG
1 TTAAACCTTTGGGAAAG
73467 TTAAAGCCTTTGGGAAAG
1 TTAAA-CCTTTGGGAAAG
73485 CATAGCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (17 bp):
TTAAACCTTTGGGAAAG
Found at i:73537 original size:76 final size:77
Alignment explanation
Indices: 73437--73622 Score: 191
Period size: 76 Copynumber: 2.4 Consensus size: 77
73427 TTTAAGAATA
* * * **
73437 CAAGATGATCAATTTAAACCTTTGGGAAAGTTAAAGCCTTTGGGAAA-GCATAGCAACATTCTTG
1 CAAGATAATCAATTTGAACATTTGGGAAAGTTAAAGCCTTTGGGAAAGGCATAGCAACATTCTCA
73501 AGCCTGTA-AAGG
66 AGCCTG-AGAAGG
** ** * *
73513 TGAGATAATCAATTTGAACATTT-GGAAAGGTT-AAGGTTTTTGGAAAGGCATAGCAATATTCTC
1 CAAGATAATCAATTTGAACATTTGGGAAA-GTTAAAGCCTTTGGGAAAGGCATAGCAACATTCTC
*
73576 AAGCTTGAGAAGG
65 AAGCCTGAGAAGG
* * *
73589 CAAGATAATCAATTTGAGCTTTTGGGAAGGTTAA
1 CAAGATAATCAATTTGAACATTTGGGAAAGTTAA
73623 GGAATTTAGG
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
75 17 0.19
76 66 0.75
77 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (77 bp):
CAAGATAATCAATTTGAACATTTGGGAAAGTTAAAGCCTTTGGGAAAGGCATAGCAACATTCTCA
AGCCTGAGAAGG
Found at i:74563 original size:13 final size:13
Alignment explanation
Indices: 74545--74570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74535 CAATTTTTTG
74545 TGTATCGATACAT
1 TGTATCGATACAT
74558 TGTATCGATACAT
1 TGTATCGATACAT
74571 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:74581 original size:32 final size:33
Alignment explanation
Indices: 74525--74588 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
74515 TACAAGCCAA
*
74525 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
*
74558 TGTATCGATAC-ATATTTTGTGTATTGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
74589 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:75312 original size:21 final size:21
Alignment explanation
Indices: 75271--75314 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
75261 CTCCCCTTTA
* *
75271 TCTCCCCCTTTTATTAATAAT
1 TCTCCCCCTTTAATCAATAAT
75292 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCTTTAATCAA-TAAT
75313 TC
1 TC
75315 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (21 bp):
TCTCCCCCTTTAATCAATAAT
Found at i:76645 original size:21 final size:20
Alignment explanation
Indices: 76616--76658 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
76606 GGCTGGTGTG
**
76616 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCACGACCT
*
76637 GGGAGTGCCGGTCACGACCT
1 GGGACTGCCGGTCACGACCT
76657 GG
1 GG
76659 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCACGACCT
Found at i:77108 original size:13 final size:13
Alignment explanation
Indices: 77090--77114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77080 ATAATCCCCC
77090 TGTATCGATACAG
1 TGTATCGATACAG
77103 TGTATCGATACA
1 TGTATCGATACA
77115 ATTACAAAGA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:79221 original size:15 final size:15
Alignment explanation
Indices: 79201--79232 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
79191 ATTTCGTTTG
*
79201 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
79216 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
79231 GA
1 GA
79233 ACACTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:81064 original size:21 final size:21
Alignment explanation
Indices: 81035--81079 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
81025 AAGTTTTTAT
*
81035 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
81055 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
81077 TTT
1 TTT
81080 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:83318 original size:13 final size:13
Alignment explanation
Indices: 83300--83325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
83290 CAATTTTTTG
83300 TGTATCGATACAT
1 TGTATCGATACAT
83313 TGTATCGATACAT
1 TGTATCGATACAT
83326 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:83336 original size:32 final size:33
Alignment explanation
Indices: 83280--83343 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
83270 TACAAGCCAA
*
83280 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
83313 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
83344 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:83337 original size:19 final size:19
Alignment explanation
Indices: 83280--83343 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
83270 TACAAGCCAA
*
83280 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
83300 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
83313 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
83332 TGTATCGATACA
1 TGTATCGATACA
83344 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:85638 original size:14 final size:14
Alignment explanation
Indices: 85619--85645 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
85609 CCTAAGACAC
85619 TTTCTTTTAGATGA
1 TTTCTTTTAGATGA
85633 TTTCTTTTAGATG
1 TTTCTTTTAGATG
85646 TTAGTCAATA
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:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (14 bp):
TTTCTTTTAGATGA
Found at i:87036 original size:20 final size:20
Alignment explanation
Indices: 87008--87082 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
86998 TTTTACCCAG
87008 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* ** * *
87028 ATATATCGATACACGTATGA
1 ATGTATCGATACATTTTTCA
* * *
87048 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
87068 ATGTATCGATACATT
1 ATGTATCGATACATT
87083 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:88028 original size:20 final size:21
Alignment explanation
Indices: 87990--88028 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
87980 AGCCTTTGAC
**
87990 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAACATGTTT
88011 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
88029 CCAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:92213 original size:19 final size:18
Alignment explanation
Indices: 92189--92284 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
92179 TTTCAATGAT
92189 TTGTATCGATACATTAGTG
1 TTGTATCGATACA-TAGTG
92208 TTGTATCGATACA-A---
1 TTGTATCGATACATAGTG
92222 -TGTATCGATACATAAGTG
1 TTGTATCGATACAT-AGTG
92240 TTGTATCGATACA-A---
1 TTGTATCGATACATAGTG
* *
92254 -TGTATCGATAGATAAGTT
1 TTGTATCGATACAT-AGTG
92272 TTGTATCGATACA
1 TTGTATCGATACA
92285 ATGTACTGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
13 23 0.37
15 2 0.03
17 2 0.03
19 36 0.57
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (18 bp):
TTGTATCGATACATAGTG
Found at i:92227 original size:13 final size:13
Alignment explanation
Indices: 92209--92263 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
92199 ACATTAGTGT
92209 TGTATCGATACAA
1 TGTATCGATACAA
92222 TGTATCGATACATAA
1 TGTATCGATAC--AA
92237 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
92254 TGTATCGATA
1 TGTATCGATA
92264 GATAAGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 21 0.58
15 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:92231 original size:32 final size:32
Alignment explanation
Indices: 92190--92289 Score: 173
Period size: 32 Copynumber: 3.1 Consensus size: 32
92180 TTCAATGATT
*
92190 TGTATCGATACATTAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
92222 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
92254 TGTATCGATAGATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
92286 TGTA
1 TGTA
92290 CTGCTACGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:92355 original size:13 final size:13
Alignment explanation
Indices: 92337--92361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92327 ATTACTCAAA
92337 TGTATCGATACAT
1 TGTATCGATACAT
92350 TGTATCGATACA
1 TGTATCGATACA
92362 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:92414 original size:52 final size:52
Alignment explanation
Indices: 92370--92498 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
92360 CACTGATCTT
92370 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * * * *
92422 TGTATCGAAACATACAGGCAAATTTGCCTAGATGTATCTATACATTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
92474 TGTATCGATACATGCAGACAAATTT
1 TGTATCGATACATGCAGGCAAATTT
92499 TCATATTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:96849 original size:240 final size:239
Alignment explanation
Indices: 96425--96878 Score: 667
Period size: 240 Copynumber: 1.9 Consensus size: 239
96415 GGTTACTAAG
* *
96425 AAGCCATGATAATGGCTAAGAGCTTGACTAAGGTACAAGAATTAGTTCATTAATGATGGCCAAAA
1 AAGCCATGATAATGACTAAGAGCTTGACTAAAGTACAAGAATTAGTTCATTAATGATGGCCAAAA
* * * ** *
96490 AGGTTGCTTGGTTCCTCTTAAGTGGTCATTAAAAGCTCAAGGGCTATGGTTGGTGATGTATTACA
66 AGGTTGCTTGGTTCCTCTCAAATGGTCATTAAAAGCTCAAAGGCTATGGTCAGTGATGTACTACA
* ** * *
96555 TCACCAAAGTGGAAGAGGCTGGTGATTGGGATTAGAATAATAACAAAGACATGGCTTTCTCATAG
131 TCACCAAAGTGGAAGAGACTGGTGATTAAGATTAGAATAACAACAAAGACATGGCTTTCTCATAA
*
96620 ACAATGTCAAATTATTGATTTTTTTTTTTTGGTTGGTTGTTAAA
196 ACAACGTCAAATTATTGATTTTTTTTTTTTGGTTGGTTGTTAAA
* * * *
96664 AAGCCATGATAATGATTAGGAGTTTGACTAAAGTACAAGAATTAGTTCATTAATGATGGCTAAAA
1 AAGCCATGATAATGACTAAGAGCTTGACTAAAGTACAAGAATTAGTTCATTAATGATGGCCAAAA
* *
96729 GGGGTTGTTTGGTTCCTCTCAAATGGTCATTAAGAA-CTCAAAGGCTATGGTCAGTGATGTACTA
66 -AGGTTGCTTGGTTCCTCTCAAATGGTCATTAA-AAGCTCAAAGGCTATGGTCAGTGATGTACTA
* * *
96793 CATCACCAAAGTGGAAGAGACTGGTGATTAAGATTAGAATAACAGCAAATACATGGCTTTTTCAT
129 CATCACCAAAGTGGAAGAGACTGGTGATTAAGATTAGAATAACAACAAAGACATGGCTTTCTCAT
*
96858 AAACAACGTTAAATTATTGAT
194 AAACAACGTCAAATTATTGAT
96879 GTCTTTTTAA
Statistics
Matches: 189, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
239 59 0.31
240 128 0.68
241 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (239 bp):
AAGCCATGATAATGACTAAGAGCTTGACTAAAGTACAAGAATTAGTTCATTAATGATGGCCAAAA
AGGTTGCTTGGTTCCTCTCAAATGGTCATTAAAAGCTCAAAGGCTATGGTCAGTGATGTACTACA
TCACCAAAGTGGAAGAGACTGGTGATTAAGATTAGAATAACAACAAAGACATGGCTTTCTCATAA
ACAACGTCAAATTATTGATTTTTTTTTTTTGGTTGGTTGTTAAA
Found at i:99340 original size:38 final size:34
Alignment explanation
Indices: 99292--99372 Score: 101
Period size: 33 Copynumber: 2.3 Consensus size: 34
99282 ACTAATTAAA
*
99292 TTTAAAAAATTTAATAAATAATATATTAATTATTATTT
1 TTTAAAAAA-TTAA-AAATAATAT-TTAATAATT-TTT
*
99330 TTTATAAAATTAAAAATAATATTTAATAA-TTTT
1 TTTAAAAAATTAAAAATAATATTTAATAATTTTT
99363 TTTAAAAAAT
1 TTTAAAAAAT
99373 AAGATATGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 12 0.30
34 1 0.03
35 6 0.15
36 9 0.22
37 4 0.10
38 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
TTTAAAAAATTAAAAATAATATTTAATAATTTTT
Found at i:99684 original size:21 final size:22
Alignment explanation
Indices: 99638--99687 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
99628 ATTATTACTT
***
99638 TTTATTTATAAATTAATTTTAA
1 TTTATTTATAAATTAATACAAA
99660 TTTATTTATAAATT-ATACAAA
1 TTTATTTATAAATTAATACAAA
99681 TTTATTT
1 TTTATTT
99688 TTATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTTATAAATTAATACAAA
Found at i:99728 original size:43 final size:44
Alignment explanation
Indices: 99593--99728 Score: 109
Period size: 43 Copynumber: 3.1 Consensus size: 44
99583 TTTACATGTG
* *
99593 TTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACTTT
1 TTATTTTTATTAAAATTAATTAATATTGTACATGTATTACT--TTT
* ** * * * ***
99639 TTATTTATAAATTAATTTTAATTTAT-TTATAAAT-TA-TACAAAT
1 TTATTT-T-TATTAAAATTAATTAATATTGTACATGTATTACTTTT
99682 TTATTTTTATTAAAATTAATTAATATTGTACATGTATTA-TTTT
1 TTATTTTTATTAAAATTAATTAATATTGTACATGTATTACTTTT
99725 TTAT
1 TTAT
99729 AATTGATAAA
Statistics
Matches: 65, Mismatches: 20, Indels: 13
0.66 0.20 0.13
Matches are distributed among these distances:
41 13 0.20
42 7 0.11
43 14 0.22
44 2 0.03
45 2 0.03
46 8 0.12
47 6 0.09
48 13 0.20
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57
Consensus pattern (44 bp):
TTATTTTTATTAAAATTAATTAATATTGTACATGTATTACTTTT
Found at i:99898 original size:299 final size:298
Alignment explanation
Indices: 99518--100177 Score: 996
Period size: 299 Copynumber: 2.2 Consensus size: 298
99508 TATATGTATT
* ** * *
99518 ATTTTTTGATAACAACTTAAATACGAGTTTTTCTTTATATGTAAAATGACTAAGAAAAAATTTAT
1 ATTTTTCGATAATGACTTAAATACGAGTTTTTCTTTATCTATAAAATGACTAAGAAAAAATTTAT
* * *
99583 TTTACATGTGTTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACTTTTTATTTATA
66 TATACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGCATTATTACTTTTTATTTATA
99648 AATTAATTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
131 AATTAATTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
* * *
99713 ATGTATTATTTTTTATAATTGATAAAATTTAAATTTATGTTAGCCAACAATAAATTATTTTTTTC
196 ATGTATTA-TTTTTATAATTAATAAAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTTC
* * * * * * *
99778 GATAACGATTTATTTCGGATTTATAGACGTACGCATTTC
260 CATAACGACTTATTTCGAATTTAAAGAAGCACACATTTC
* * * *
99817 ATTTTTCGGTAATGTCTTAAATACAAGTTTTCCTTTATCTATAAAATGACTAAGAAAAAATTTAT
1 ATTTTTCGATAATGACTTAAATACGAGTTTTTCTTTATCTATAAAATGACTAAGAAAAAATTTAT
* * *
99882 TATATATTTATTATTTTTATTAAAATTAATTGATATTGTGCATGCATTATTACTTTTTATTTATA
66 TATACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGCATTATTACTTTTTATTTATA
* * *
99947 AATTATTTTTAATTTATTTGTAAATTATATAAATTTATTTTTATTAAAATTAATTAATATTGTAC
131 AATTAATTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
* * * *
100012 ATGTCTTATTTTTATAATTAATAGAACTTAAATTTATGTTTGTCAACAATAAATTACTTTTTTCC
196 ATGTATTATTTTTATAATTAATAAAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTTCC
* *
100077 ATAATGACTTATTTCGAATTTAAAGAAGCACACATTTT
261 ATAACGACTTATTTCGAATTTAAAGAAGCACACATTTC
*
100115 ATTTTTCGATAATGACTTAAATACGAGTTTTTCTTTATCTATAAAAAGACTAAGAAAAAATTT
1 ATTTTTCGATAATGACTTAAATACGAGTTTTTCTTTATCTATAAAATGACTAAGAAAAAATTT
100178 TCCTCAACTT
Statistics
Matches: 322, Mismatches: 39, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
298 138 0.43
299 184 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (298 bp):
ATTTTTCGATAATGACTTAAATACGAGTTTTTCTTTATCTATAAAATGACTAAGAAAAAATTTAT
TATACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGCATTATTACTTTTTATTTATA
AATTAATTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
ATGTATTATTTTTATAATTAATAAAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTTCC
ATAACGACTTATTTCGAATTTAAAGAAGCACACATTTC
Found at i:103818 original size:95 final size:92
Alignment explanation
Indices: 103643--104678 Score: 729
Period size: 92 Copynumber: 11.4 Consensus size: 92
103633 TTCAATTGTG
* * * *** * * ** * *
103643 ATATTTACAATCAATTAACTTTTCAGCTTTTGTATCAAAAAGAATTTGATTCTCAAATAAAATTT
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
* *
103708 ATGCATTAGTCTAATCTTTGCAGTGTG
66 ATGCATTAGTCTAATCTTTGCAGTATA
* * * * **
103735 AT-TCTTATAATCAA-CAAACTTTTCTTCTTTTTTTTTACCAAAAGAAATCCGATTCTCATGTAC
1 ATAT-TTATAATCAATC-AACTTTCCTT-TTTTTATATA-AAAAAG-AATCCGATTCTCAAATAC
* *
103798 AATTCATGTATTAGTCTAATCCTTGCAGTATA
61 AATTCATGCATTAGTCTAATCTTTGCAGTATA
* * *
103830 ATATTTATAATCAATCAGCTTTCCTTTTTTTATATAAAAAAGAATCTGATTCTCAAATATAATTC
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
** * *
103895 ATGCATTAGTCTAATCTTTATAGTCTC
66 ATGCATTAGTCTAATCTTTGCAGTATA
* * * * * * * * * * *
103922 ACATTTACAATTAGTTAACTTTTCTTTTTTTCTATAAAAAAGACTCCGATTCTCAGATATAATTT
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
* * *
103987 ATACATTAGTCTAAT-TGTTGTAGTCTA
66 ATGCATTAGTCTAATCT-TTGCAGTATA
* * * * * *
104014 ACATTTATAATCAATCAA-TCTT--TTTTTTTATCTAAGAAAGAATCTGATTCTCAGATATAATT
1 ATATTTATAATCAATCAACT-TTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATT
* * *
104076 CATGCATTAGTCTAATCATTGCAGTTTG
65 CATGCATTAGTCTAATCTTTGCAGTATA
* * * * * * *
104104 ACATTTACAATTAGTCAAC--T--TTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTC
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
* * * * *
104165 ATGCACTAGTCTAATCCTTGTAATGTA
66 ATGCATTAGTCTAATCTTTGCAGTATA
* * * * * * * * *
104192 ACATTTATAATTAATCAATTTTTC-TTTTTTCTACAAAAAAGAATCTGATTCTCAGATATAATTC
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
* * * * * *
104256 ATGTACTAGTCTAATCATCGCAGTCTG
66 ATGCATTAGTCTAATCTTTGCAGTATA
* * * * *
104283 ACATTTACAATCAATCAACTTTTCTTTTTTGT-CATAAAAAAGAATCCGATTCTCAAATATAATT
1 ATATTTATAATCAATCAACTTTCCTTTTTT-TATATAAAAAAGAATCCGATTCTCAAATACAATT
* * * *
104347 CGTGCATTAGTCTAATCTTTGTAGTTTG
65 CATGCATTAGTCTAATCTTTGCAGTATA
* * * * *
104375 ACATTTATAATCAGTCAAC--T--TTTTTTTA-ATAAAAAAGAATCCGATTCTTAGATATAATTC
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
* * *
104435 ATGCATTAGTCTAAT-TCCTGTAGTACA
66 ATGCATTAGTCTAATCT-TTGCAGTATA
* * * *** * *
104462 ACATTTATAATCAATCAAC--T--TTTTTTT-TGTAAAAAATAATTTAATTCTCAGATATAATTC
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
* * *
104522 ATGCATTAGTCTAATCCTTGCAGTCTG
66 ATGCATTAGTCTAATCTTTGCAGTATA
* * * * *
104549 ACATTTACAATCAATCAACTTT-TTTTTATTTA-ATAAAAAAGAATCTGATTCTCAAATATAATT
1 ATATTTATAATCAATCAACTTTCCTTTT-TTTATATAAAAAAGAATCCGATTCTCAAATACAATT
* * *
104612 CATGCATTAGTTTAATCTTTGCAGTTTG
65 CATGCATTAGTCTAATCTTTGCAGTATA
* * * *
104640 ACATTTACAATCAATCAACTTTTCTTTTTCTATA-AAAAA
1 ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAA
104679 GTCTGATTTT
Statistics
Matches: 780, Mismatches: 136, Indels: 57
0.80 0.14 0.06
Matches are distributed among these distances:
86 1 0.00
87 141 0.18
88 81 0.10
89 1 0.00
90 77 0.10
91 166 0.21
92 226 0.29
93 12 0.02
94 13 0.02
95 60 0.08
96 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (92 bp):
ATATTTATAATCAATCAACTTTCCTTTTTTTATATAAAAAAGAATCCGATTCTCAAATACAATTC
ATGCATTAGTCTAATCTTTGCAGTATA
Found at i:104198 original size:270 final size:267
Alignment explanation
Indices: 103679--104698 Score: 1081
Period size: 270 Copynumber: 3.8 Consensus size: 267
103669 CTTTTGTATC
* * * * * * * *
103679 AAAAAGAATTTGATTCTCAAATAAAATTTATGCATTAGTCTAATCTTTGCAGTGTGA-TTCTTAT
1 AAAAAG-ATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCATTGCAGTCTGACAT-TTAC
* * * * ** * *
103743 AATCAA-CAAACTTTTCTTCTTTTTTTTTACCAAAAGAAATCCGATTCTCATGTACAATTCATGT
64 AATCAATC-AAC--TT-TT-TTTTTATCTA-AAAAAG-AATCTGATTCTCAAATATAATTCATGC
* * * * * * * *
103807 ATTAGTCTAATCCTTGCAGTATAATATTTATAATCAATCAGCTTTCCTTTTTTTATATAAAAAAG
122 ATTAGTCTAATCTTTGCAGTTTGACATTTACAATCAGTCAAC--T--TTTTTTTCTATAAAAAAG
* * * * * * * *
103872 AATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTATAGTCTCACATTTACAATTAGT
183 AATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGTAGTATAACATTTATAATTAAT
*
103937 TAACTTTTCTTTTTTTCTATA
248 CAACTTTTCTTTTTTTCTA-A
* * * ** * * *
103958 AAAAAGACTCCGATTCTCAGATATAATTTATACATTAGTCTAATTGTTGTAGTCTAACATTTATA
1 AAAAAGA-TCTGATTCTCAGATATAATTCATGCATTAGTCTAATCATTGCAGTCTGACATTTACA
* *
104023 ATCAATCAATCTTTTTTTTTATCTAAGAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTC
65 ATCAATCAA-CTTTTTTTTTATCTAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTC
* *
104088 TAATCATTGCAGTTTGACATTTACAATTAGTCAACTTTTTTTTCTATAAAAAAGAATCCGATTCT
129 TAATCTTTGCAGTTTGACATTTACAATCAGTCAACTTTTTTTTCTATAAAAAAGAATCCGATTCT
* * * *
104153 CAGATATAATTCATGCACTAGTCTAATCCTTGTAATGTAACATTTATAATTAATCAATTTTTC-T
194 CAGATATAATTCATGCATTAGTCTAATCCTTGTAGTATAACATTTATAATTAATCAACTTTTCTT
104217 TTTTTCTACA
259 TTTTTCTA-A
* * *
104227 AAAAAGAATCTGATTCTCAGATATAATTCATGTACTAGTCTAATCATCGCAGTCTGACATTTACA
1 AAAAAG-ATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCATTGCAGTCTGACATTTACA
* * *
104292 ATCAATCAACTTTTCTTTTTTGTCATAAAAAAGAATCCGATTCTCAAATATAATTCGTGCATTAG
65 ATCAATCAAC-TTT-TTTTTTATC-TAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAG
* * *
104357 TCTAATCTTTGTAGTTTGACATTTATAATCAGTCAACTTTTTTTT-AATAAAAAAGAATCCGATT
127 TCTAATCTTTGCAGTTTGACATTTACAATCAGTCAACTTTTTTTTCTATAAAAAAGAATCCGATT
* * *
104421 CTTAGATATAATTCATGCATTAGTCTAATTCC-TGTAGTACAACATTTATAATCAATCAAC--TT
192 CTCAGATATAATTCATGCATTAGTCTAA-TCCTTGTAGTATAACATTTATAATTAATCAACTTTT
*
104483 -TTTTTTTGTAA
256 CTTTTTTTCTAA
* * *
104494 AAAATA-ATTTAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACA
1 AAAA-AGATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCATTGCAGTCTGACATTTACA
* *
104558 ATCAATCAACTTTTTTTTATTTAATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGT
65 ATCAATCAACTTTTTTTT-TAT-CTAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGT
* * *
104623 TTAATCTTTGCAGTTTGACATTTACAATCAATCAACTTTTCTTTTTCTATAAAAAAG--TCTGAT
128 CTAATCTTTGCAGTTTGACATTTACAATCAGTCAAC-TTT-TTTTTCTATAAAAAAGAATCCGAT
*
104686 TTTCAGATATAAT
191 TCTCAGATATAAT
104699 CATATTTATT
Statistics
Matches: 636, Mismatches: 89, Indels: 45
0.83 0.12 0.06
Matches are distributed among these distances:
264 5 0.01
265 76 0.12
266 81 0.13
267 10 0.02
268 21 0.03
269 74 0.12
270 155 0.24
271 80 0.13
272 1 0.00
274 56 0.09
275 4 0.01
276 8 0.01
277 2 0.00
278 3 0.00
279 57 0.09
280 3 0.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (267 bp):
AAAAAGATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCATTGCAGTCTGACATTTACAA
TCAATCAACTTTTTTTTTATCTAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTA
ATCTTTGCAGTTTGACATTTACAATCAGTCAACTTTTTTTTCTATAAAAAAGAATCCGATTCTCA
GATATAATTCATGCATTAGTCTAATCCTTGTAGTATAACATTTATAATTAATCAACTTTTCTTTT
TTTCTAA
Found at i:104440 original size:87 final size:88
Alignment explanation
Indices: 103761--104698 Score: 897
Period size: 92 Copynumber: 10.5 Consensus size: 88
103751 AACTTTTCTT
** * * * *
103761 CTTTTTTTTTACCAAAAGA-AATCCGATTCTCATG-TACAATTCATGTATTAGTCTAATCCTTGC
1 CTTTTTTTTTAATAAAAAAGAATCCGATTCTCA-GATATAATTCATGCATTAGTCTAATCTTTGC
* * * * *
103824 AGTATAATATTTATAATCAATCAG
65 AGTCTGACATTTACAATCAATCAA
* *
103848 CTTTCCTTTTTTTATATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTT
1 C-TT--TTTTTTTA-ATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTT
** * * * *
103913 TATAGTCTCACATTTACAATTAGTTAA
62 TGCAGTCTGACATTTACAATCAATCAA
* * * *
103940 CTTTTCTTTTTTTCTATAAAAAAGACTCCGATTCTCAGATATAATTTATACATTAGTCTAAT-TG
1 C--TT-TTTTTTT-AATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCT-
* * *
104004 TTGTAGTCTAACATTTATAATCAATCAA
61 TTGCAGTCTGACATTTACAATCAATCAA
* * * *
104032 TCTTTTTTTTTATCTAAGAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCATTG
1 -CTTTTTTTTTA-ATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTG
* * *
104097 CAGTTTGACATTTACAATTAGTCAA
64 CAGTCTGACATTTACAATCAATCAA
* * *
104122 CTTTTTTTTCT-ATAAAAAAGAATCCGATTCTCAGATATAATTCATGCACTAGTCTAATCCTTGT
1 CTTTTTTTT-TAATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGC
* * * * *
104186 AATGTAACATTTATAATTAATCAA
65 AGTCTGACATTTACAATCAATCAA
* * * * * * * *
104210 TTTTTCTTTTTTCTACAAAAAAGAATCTGATTCTCAGATATAATTCATGTACTAGTCTAATCATC
1 -CTTT-TTTTTT-AATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTT
104275 GCAGTCTGACATTTACAATCAATCAA
63 GCAGTCTGACATTTACAATCAATCAA
* * *
104301 CTTTTCTTTTTTGTCATAAAAAAGAATCCGATTCTCAAATATAATTCGTGCATTAGTCTAATCTT
1 C--TT-TTTTTT-TAATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTT
* * * *
104366 TGTAGTTTGACATTTATAATCAGTCAA
62 TGCAGTCTGACATTTACAATCAATCAA
* * *
104393 C-TTTTTTTTAATAAAAAAGAATCCGATTCTTAGATATAATTCATGCATTAGTCTAAT-TCCTGT
1 CTTTTTTTTTAATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCT-TTGC
* *
104456 AGTAC-AACATTTATAATCAATCAA
65 AGT-CTGACATTTACAATCAATCAA
* * *** *
104480 CTTTTTTTTT-GTAAAAAATAATTTAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCA
1 CTTTTTTTTTAATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGCA
104544 GTCTGACATTTACAATCAATCAA
66 GTCTGACATTTACAATCAATCAA
* * *
104567 CTTTTTTTTATTTAATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTTTAATCTTT
1 C--TTTTTT-TTTAATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTT
*
104632 GCAGTTTGACATTTACAATCAATCAA
63 GCAGTCTGACATTTACAATCAATCAA
* * *
104658 CTTTTCTTTTTCTATAAAAAAG--TCTGATTTTCAGATATAAT
1 CTTTT-TTTTT-AATAAAAAAGAATCCGATTCTCAGATATAAT
104699 CATATTTATT
Statistics
Matches: 708, Mismatches: 111, Indels: 63
0.80 0.13 0.07
Matches are distributed among these distances:
86 2 0.00
87 134 0.19
88 99 0.14
89 27 0.04
90 98 0.14
91 144 0.20
92 198 0.28
93 6 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (88 bp):
CTTTTTTTTTAATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGCA
GTCTGACATTTACAATCAATCAA
Found at i:104811 original size:24 final size:24
Alignment explanation
Indices: 104779--104908 Score: 107
Period size: 24 Copynumber: 5.1 Consensus size: 24
104769 CCTTACGATC
104779 TAATATAAATAAATTTGTATAATT
1 TAATATAAATAAATTTGTATAATT
104803 TAATATAAATAAATTTGTATAATT
1 TAATATAAATAAATTTGTATAATT
* * * *
104827 TAATAAAAATTAATAATACATGCACAATAT
1 TAATATAAA-T-A-AAT--TTGTATAAT-T
****
104857 TAATTATAAATAAATTACCCTAATTT
1 TAA-TATAAATAAATTTGTATAA-TT
*
104883 TAATAAAAATAAATTTGTATAATT
1 TAATATAAATAAATTTGTATAATT
104907 TA
1 TA
104909 TAAGTAAATT
Statistics
Matches: 83, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
24 36 0.43
25 15 0.18
26 8 0.10
27 4 0.05
28 3 0.04
29 7 0.08
30 5 0.06
31 5 0.06
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (24 bp):
TAATATAAATAAATTTGTATAATT
Found at i:105203 original size:46 final size:44
Alignment explanation
Indices: 105153--105281 Score: 113
Period size: 44 Copynumber: 2.9 Consensus size: 44
105143 AATTATAAAA
* * *
105153 ATAATACATGTACAATATTAATTAATTTTAATAAAAATAAATTTG
1 ATAATATATGAACAATATTAATTAATTTTAATAAAAATAAA-ATG
* * * *
105198 TATAATTTATAAATAA-ATTAA-AAATAATTT-ATAAATAA-AAAATG
1 -ATAATATATGAACAATATTAATTAAT--TTTAATAAA-AATAAAATG
*
105242 ATAATATATGCACAATATTAATTAATTTTAATAAAAATAA
1 ATAATATATGAACAATATTAATTAATTTTAATAAAAATAA
105282 TACATGAACA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
43 16 0.25
44 17 0.27
45 16 0.25
46 15 0.23
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (44 bp):
ATAATATATGAACAATATTAATTAATTTTAATAAAAATAAAATG
Found at i:106303 original size:3 final size:3
Alignment explanation
Indices: 106295--106325 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
106285 AGGCCTACAA
*
106295 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
106326 GTAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:111982 original size:10 final size:10
Alignment explanation
Indices: 111959--112214 Score: 172
Period size: 10 Copynumber: 26.0 Consensus size: 10
111949 ATTCAATATT
* *
111959 GTGTGTGTGT
1 GTGTGCGTGC
111969 GTGTGCGTGC
1 GTGTGCGTGC
* * *
111979 GTGTACATGT
1 GTGTGCGTGC
*
111989 GCGTGCGTGC
1 GTGTGCGTGC
111999 GTGTGCGTGC
1 GTGTGCGTGC
112009 GTGT--GTGC
1 GTGTGCGTGC
* * *
112017 GTGCGTGTTC
1 GTGTGCGTGC
*
112027 ATGTGCGTGC
1 GTGTGCGTGC
*
112037 GCGTGCGTGC
1 GTGTGCGTGC
*
112047 GTGGGCGTGC
1 GTGTGCGTGC
*
112057 GCGTGCGTGC
1 GTGTGCGTGC
*
112067 GTGGGCGTGC
1 GTGTGCGTGC
112077 GTGTGCGTGCGC
1 GTGTGCGT--GC
112089 GTGTGCGTGC
1 GTGTGCGTGC
112099 GTGTGCGT--
1 GTGTGCGTGC
112107 GTGTGCGTGC
1 GTGTGCGTGC
*
112117 --GTGCGCGC
1 GTGTGCGTGC
*
112125 TTGTGCGTGTGC
1 GTGTGC--GTGC
*
112137 ATGTGTGTGTGC
1 --GTGTGCGTGC
*
112149 GTGTGC--AC
1 GTGTGCGTGC
*
112157 GTGTGTGTGC
1 GTGTGCGTGC
*
112167 GTGTGCAT--
1 GTGTGCGTGC
*
112175 GTGTGTGTGC
1 GTGTGCGTGC
112185 GTGTGCGTGC
1 GTGTGCGTGC
* *
112195 GTGTGTGTGT
1 GTGTGCGTGC
*
112205 GTGCGCGTGC
1 GTGTGCGTGC
112215 ATGCATGTTA
Statistics
Matches: 187, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
8 34 0.18
10 132 0.71
12 17 0.09
14 4 0.02
ACGTcount: A:0.02, C:0.18, G:0.48, T:0.32
Consensus pattern (10 bp):
GTGTGCGTGC
Found at i:111989 original size:16 final size:14
Alignment explanation
Indices: 111970--112141 Score: 85
Period size: 16 Copynumber: 12.3 Consensus size: 14
111960 TGTGTGTGTG
111970 TGTGCGTGCGTGTACA
1 TGTGCGTGCGTG--CA
*
111986 TGTGCGTGCGTGCG
1 TGTGCGTGCGTGCA
112000 TGTGCGTGCGTG--
1 TGTGCGTGCGTGCA
112012 TGTGCGTGCGTGTTCA
1 TGTGCGTGCGTG--CA
112028 TGTGCGTGC--GC-
1 TGTGCGTGCGTGCA
*
112039 -GTGCGTGCGTGGGCG
1 TGTGCGTGCGT--GCA
* *
112054 TGCGCGTGCGTGCG
1 TGTGCGTGCGTGCA
* *
112068 TGGGCGTGCGTGTGCG
1 TGTGCGTGC--GTGCA
* *
112084 TGCGCGTGTGCGTGCG
1 TGTGC--GTGCGTGCA
*
112100 TGTGCGTGTGTGC-
1 TGTGCGTGCGTGCA
* *
112113 -GTGCGTGCGCGCT
1 TGTGCGTGCGTGCA
112126 TGTGCGT--GTGCA
1 TGTGCGTGCGTGCA
112138 TGTG
1 TGTG
112142 TGTGTGCGTG
Statistics
Matches: 130, Mismatches: 10, Indels: 36
0.74 0.06 0.20
Matches are distributed among these distances:
10 8 0.06
12 30 0.23
14 40 0.31
16 48 0.37
18 4 0.03
ACGTcount: A:0.02, C:0.21, G:0.48, T:0.29
Consensus pattern (14 bp):
TGTGCGTGCGTGCA
Found at i:111994 original size:4 final size:4
Alignment explanation
Indices: 111987--112121 Score: 100
Period size: 4 Copynumber: 36.2 Consensus size: 4
111977 GCGTGTACAT
*
111987 GTGC GTGC GTGC GT-- GTGC GTGC GTGT GTGC GTGC GTGTTC ATGTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTG--C --GTGC
112033 GTGC --GC GTGC GTGC GTG- G-GC GTGC --GC GTGC GTGC GTG- G-GC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
* * *
112073 GTGC GT-- GTGC GTGC GCGT GTGC GTGC GT-- GTGC GTGT GTGC GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
112117 GTGC G
1 GTGC G
112122 CGCTTGTGCG
Statistics
Matches: 105, Mismatches: 8, Indels: 36
0.70 0.05 0.24
Matches are distributed among these distances:
2 12 0.11
3 4 0.04
4 84 0.80
6 2 0.02
8 3 0.03
ACGTcount: A:0.01, C:0.21, G:0.50, T:0.27
Consensus pattern (4 bp):
GTGC
Found at i:112008 original size:18 final size:18
Alignment explanation
Indices: 111987--112209 Score: 171
Period size: 18 Copynumber: 12.1 Consensus size: 18
111977 GCGTGTACAT
*
111987 GTGCGTGCGTGCGTGTGC
1 GTGCGTGTGTGCGTGTGC
* *
112005 GTGCGTGTGTGCGTGCGT
1 GTGCGTGTGTGCGTGTGC
* * *
112023 GTTCATGTGCGTGCGCGTGC
1 GTGC--GTGTGTGCGTGTGC
* *
112043 GTGCGTGGGCGTGCGCGTGC
1 GTGCGT--GTGTGCGTGTGC
*
112063 GTGCGTGGGCGTGCGTGTGC
1 GTGCGT--GTGTGCGTGTGC
* * *
112083 GTGCGCGTGTGCGTGCGT
1 GTGCGTGTGTGCGTGTGC
112101 GTGCGTGTGTGC--GTGC
1 GTGCGTGTGTGCGTGTGC
*
112117 GTGCGCGCTTGTGCGTGTGC
1 GTGCGTG--TGTGCGTGTGC
* *
112137 ATGTGTGTGTGCGTGTGC
1 GTGCGTGTGTGCGTGTGC
** *
112155 ACGTGTGTGTGCGTGTGC
1 GTGCGTGTGTGCGTGTGC
* *
112173 ATGTGTGTGTGCGTGTGC
1 GTGCGTGTGTGCGTGTGC
*
112191 GTGCGTGTGTGTGTGTGC
1 GTGCGTGTGTGCGTGTGC
112209 G
1 G
112210 CGTGCATGCA
Statistics
Matches: 171, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.05
18 106 0.62
20 57 0.33
ACGTcount: A:0.02, C:0.19, G:0.48, T:0.31
Consensus pattern (18 bp):
GTGCGTGTGTGCGTGTGC
Found at i:112143 original size:2 final size:2
Alignment explanation
Indices: 112138--112207 Score: 50
Period size: 2 Copynumber: 35.0 Consensus size: 2
112128 TGCGTGTGCA
* ** * * **
112138 TG TG TG TG TG CG TG TG CA CG TG TG TG TG CG TG TG CA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
112180 TG TG CG TG TG CG TG CG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
112208 CGCGTGCATG
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.03, C:0.11, G:0.47, T:0.39
Consensus pattern (2 bp):
TG
Found at i:112203 original size:42 final size:43
Alignment explanation
Indices: 111963--112217 Score: 186
Period size: 42 Copynumber: 5.9 Consensus size: 43
111953 AATATTGTGT
* * *
111963 GTGTGTGTGTGCGTGCGTGTACATGTGCGT--GCGTGCGTGTGC
1 GTGTGCGTGTGCGTGCGTGT-CGTGTGCGTGCGCGTGCATGTGC
* * *
112005 GTGCGTGTGTGCGTGCGTGTTCATGTGCGTGCGCGTGC--GTGC
1 GTGTGCGTGTGCGTGCGTG-TCGTGTGCGTGCGCGTGCATGTGC
* * * * * *
112047 GTGGGCGTGCGCGTGCGTG-CGTGGGCGTGCGTGTGCGTGCGC
1 GTGTGCGTGTGCGTGCGTGTCGTGTGCGTGCGCGTGCATGTGC
* * *
112089 GTGTGCGTGCGTGTGCGTGT-GTGCGTGCGTGCGC--GCTTGTGC
1 GTGTGCGTGTGCGTGCGTGTCGT--GTGCGTGCGCGTGCATGTGC
* * * *
112131 GTGTGCATGTGTGTGTGCGTGTGCACGTGTGTGTGCGTGTGCATGTGT
1 GTGTGC--GTGTGCGTGCGTGT---CGTGTGCGTGCGCGTGCATGTGC
*
112179 GTGTGCGTGTGCGTGCGTGT-GTGTGTGTGCGCGTGCATG
1 GTGTGCGTGTGCGTGCGTGTCGTGTGCGTGCGCGTGCATG
112218 CATGTTAAAA
Statistics
Matches: 176, Mismatches: 21, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
40 14 0.08
42 99 0.56
43 1 0.01
44 27 0.15
46 21 0.12
48 14 0.08
ACGTcount: A:0.03, C:0.18, G:0.47, T:0.31
Consensus pattern (43 bp):
GTGTGCGTGTGCGTGCGTGTCGTGTGCGTGCGCGTGCATGTGC
Found at i:112305 original size:28 final size:28
Alignment explanation
Indices: 112250--112349 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
112240 GTGTGTGTGG
*
112250 GCGTGCACGTGTGCGAGTGGGTGGGCGT
1 GCGTGCACGTGCGCGAGTGGGTGGGCGT
* * * *
112278 GCGTGCACGTGCGCGTGCGTGTGTGCGTGT
1 GCGTGCACGTGCGC--GAGTGGGTGGGCGT
* * *
112308 GCATGCACGTGTGCGAGTGGGTGGGTGT
1 GCGTGCACGTGCGCGAGTGGGTGGGCGT
112336 GCGTGCACGTGCGC
1 GCGTGCACGTGCGC
112350 ACATGCGCAC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 36 0.62
30 22 0.38
ACGTcount: A:0.07, C:0.21, G:0.49, T:0.23
Consensus pattern (28 bp):
GCGTGCACGTGCGCGAGTGGGTGGGCGT
Found at i:112316 original size:58 final size:58
Alignment explanation
Indices: 112239--112349 Score: 186
Period size: 58 Copynumber: 1.9 Consensus size: 58
112229 AGAGTAATAT
* *
112239 TGTGTGTGTGGGCGTGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGCGTGCG
1 TGTGTGCGTGGGCATGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGCGTGCG
* *
112297 TGTGTGCGTGTGCATGCACGTGTGCGAGTGGGTGGGTGTGCGTGCACGTGCGC
1 TGTGTGCGTGGGCATGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGC
112350 ACATGCGCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.06, C:0.19, G:0.50, T:0.25
Consensus pattern (58 bp):
TGTGTGCGTGGGCATGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGCGTGCG
Found at i:112366 original size:58 final size:56
Alignment explanation
Indices: 112244--112367 Score: 149
Period size: 58 Copynumber: 2.1 Consensus size: 56
112234 AATATTGTGT
* * * ***
112244 GTGTGGGCGTGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGCGTGCGTGT
1 GTGTGTGCATGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGCATGCGCAC
*
112300 GTGCGTGTGCATGCACGTGTGCGAGTGGGTGGGTGTGCGTGCACGTGCGCACATGCGCAC
1 GT--GTGTGCATGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCG--CATGCGCAC
112360 GTGTGTGC
1 GTGTGTGC
112368 GTGTGCGCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
56 2 0.04
58 48 0.84
60 7 0.12
ACGTcount: A:0.08, C:0.21, G:0.48, T:0.23
Consensus pattern (56 bp):
GTGTGTGCATGCACGTGTGCGAGTGGGTGGGCGTGCGTGCACGTGCGCATGCGCAC
Found at i:114108 original size:76 final size:76
Alignment explanation
Indices: 113970--114117 Score: 233
Period size: 76 Copynumber: 1.9 Consensus size: 76
113960 ATAAACCCTG
* *
113970 CCCTCTTAGCAAGTTCATGAAGCTTAATTCCCATATCTAACTTAGTTAAAGTGATCTCCTCATGC
1 CCCTCTTAGCAAGTTCATGAAGCTTAATTCCCATATCTAACTAAGTTAAAGTGATATCCTCATGC
114035 ATGAAACTCTA
66 ATGAAACTCTA
* * * **
114046 CCCTCTTAGCAAGTTCATGAAGCTTAATTCCCGTATCTGACTAAGTTAAAGTGATATTCTCATTT
1 CCCTCTTAGCAAGTTCATGAAGCTTAATTCCCATATCTAACTAAGTTAAAGTGATATCCTCATGC
114111 ATGAAAC
66 ATGAAAC
114118 CCTGCAGCTC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 65 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (76 bp):
CCCTCTTAGCAAGTTCATGAAGCTTAATTCCCATATCTAACTAAGTTAAAGTGATATCCTCATGC
ATGAAACTCTA
Found at i:117555 original size:2 final size:2
Alignment explanation
Indices: 117548--117583 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
117538 CTGATGACTA
117548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117584 GAGGTCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118139 original size:50 final size:50
Alignment explanation
Indices: 118075--118260 Score: 250
Period size: 50 Copynumber: 3.7 Consensus size: 50
118065 TTTATTAACC
* *
118075 TTTGACAATTGAGAGAGGTGATTGTAATTATTGACTATTTCTCATCAA-T
1 TTTGACAATCGAGAGAGGTGATCGTAATTATTGACTATTTCTCATCAACT
* * *
118124 CTTTGACAATCGAGAGAGGTGATCGTAATTGTTAACTATTTCTCACCAACT
1 -TTTGACAATCGAGAGAGGTGATCGTAATTATTGACTATTTCTCATCAACT
*
118175 TTTGACAATCGAGAGAGATGATCGTAATTATTGACTA-TTCTTCATCAACT
1 TTTGACAATCGAGAGAGGTGATCGTAATTATTGACTATTTC-TCATCAACT
* * * *
118225 TTTGACAATAGAGAAAGGTGACCGTAATTGTTGACT
1 TTTGACAATCGAGAGAGGTGATCGTAATTATTGACT
118261 CTAAGCATCT
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 3 0.03
50 116 0.97
51 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (50 bp):
TTTGACAATCGAGAGAGGTGATCGTAATTATTGACTATTTCTCATCAACT
Found at i:118233 original size:100 final size:100
Alignment explanation
Indices: 118075--118256 Score: 278
Period size: 100 Copynumber: 1.8 Consensus size: 100
118065 TTTATTAACC
* * * * *
118075 TTTGACAATTGAGAGAGGTGATTGTAATTATTGACTATTTCTCATCAATCTTTGACAATCGAGAG
1 TTTGACAATCGAGAGAGATGATCGTAATTATTGACTATTTCTCATCAATCTTTGACAATAGAGAA
*
118140 AGGTGATCGTAATTGTTAACTATTTCTCACCAACT
66 AGGTGACCGTAATTGTTAACTATTTCTCACCAACT
118175 TTTGACAATCGAGAGAGATGATCGTAATTATTGACTA-TTCTTCATCAA-CTTTTGACAATAGAG
1 TTTGACAATCGAGAGAGATGATCGTAATTATTGACTATTTC-TCATCAATC-TTTGACAATAGAG
118238 AAAGGTGACCGTAATTGTT
64 AAAGGTGACCGTAATTGTT
118257 GACTCTAAGC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
99 4 0.05
100 70 0.95
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (100 bp):
TTTGACAATCGAGAGAGATGATCGTAATTATTGACTATTTCTCATCAATCTTTGACAATAGAGAA
AGGTGACCGTAATTGTTAACTATTTCTCACCAACT
Found at i:122666 original size:50 final size:50
Alignment explanation
Indices: 122591--122835 Score: 382
Period size: 50 Copynumber: 4.9 Consensus size: 50
122581 GGGTGCAAAC
*
122591 GAGGTGGTCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGA
1 GAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGA
* * *
122641 GAGGTGACCATAATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGA
1 GAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGA
* * *
122691 GAGGTGGTCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATTGAGA
1 GAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGA
*
122741 GAGGTGGCCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCGAGA
1 GAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGA
* ** *
122791 AAGGTGGTTGTAATTGTTGACTATTCTTCACCAACTTTTGACAAT
1 GAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAAT
122836 AAATAAAAGT
Statistics
Matches: 178, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 178 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (50 bp):
GAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGA
Found at i:122853 original size:50 final size:50
Alignment explanation
Indices: 122600--122862 Score: 348
Period size: 50 Copynumber: 5.3 Consensus size: 50
122590 CGAGGTGGTC
*
122600 GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACC
1 GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT
* * *
122650 ATAATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGTG-GT
1 GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT
* * * *
122699 CGTAATTGTTGACTATTCCTCACCAACCTTTGACAATTGAGAGAGGTGGCC
1 -GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT
* * **
122750 GTAATTGTTGACTATTCCTCACCAACCTTTGACAATCGAGAAAGGTGGTT
1 GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT
* ** * * *
122800 GTAATTGTTGACTATTCTTCACCAACTTTTGACAATAAATAAAAGTGACT
1 GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT
122850 GTAATTGTTGACT
1 GTAATTGTTGACT
122863 CTAAGCATCT
Statistics
Matches: 189, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
50 189 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (50 bp):
GTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT
Found at i:123125 original size:14 final size:14
Alignment explanation
Indices: 123103--123327 Score: 224
Period size: 14 Copynumber: 15.9 Consensus size: 14
123093 ACTAAACAAT
*
123103 ATATATATATATAC
1 ATATGTATATATAC
123117 ATATGTATATATAC
1 ATATGTATATATAC
123131 --ATGTATATATAC
1 ATATGTATATATAC
*
123143 ATA--TAGATATAC
1 ATATGTATATATAC
*
123155 ATATGTATATATATAT
1 ATATG--TATATATAC
*
123171 ATATGTAGATATAC
1 ATATGTATATATAC
* *
123185 AAATGTATATATAT
1 ATATGTATATATAC
*
123199 ATATGTAGATATAC
1 ATATGTATATATAC
*
123213 ATATGTAGATATAC
1 ATATGTATATATAC
* *
123227 AAATGTATATATATAT
1 ATATG--TATATATAC
*
123243 ATATGTAGATATAC
1 ATATGTATATATAC
*
123257 ATATGTATATATAT
1 ATATGTATATATAC
*
123271 ATATGTATATATATAT
1 ATATG--TATATATAC
*
123287 ATATGTAGATATAC
1 ATATGTATATATAC
* *
123301 ATATGTAGATATAT
1 ATATGTATATATAC
123315 ATATGTATATATA
1 ATATGTATATATA
123328 TATAAAGAGG
Statistics
Matches: 177, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
12 23 0.13
14 117 0.66
16 37 0.21
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (14 bp):
ATATGTATATATAC
Found at i:123172 original size:44 final size:42
Alignment explanation
Indices: 123122--123331 Score: 192
Period size: 44 Copynumber: 5.2 Consensus size: 42
123112 TATACATATG
* *
123122 TATATATACATGTATATATACATATAGATATACATATGTATA
1 TATATATATATGTAGATATACATATAGATATACATATGTATA
*
123164 TATATATATATGTAGATATACAAAT-G-TAT--ATA--TATA
1 TATATATATATGTAGATATACATATAGATATACATATGTATA
* * * * * *
123200 TATGTAGATA--TACATAT--GTAGA--TATACAAATGTATA
1 TATATATATATGTAGATATACATATAGATATACATATGTATA
* *
123236 TATATATATATGTAGATATACATATGTATATATATATATGTATA
1 TATATATATATGTAGATATACATA--TAGATATACATATGTATA
*
123280 TATATATATATGTAGATATACATATGTAGATATATATATGTATA
1 TATATATATATGTAGATATACATA--TAGATATACATATGTATA
123324 TATATATA
1 TATATATA
123332 AAGAGGGGTC
Statistics
Matches: 137, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
32 4 0.03
34 8 0.06
36 24 0.18
38 9 0.07
40 5 0.04
41 1 0.01
42 23 0.17
44 63 0.46
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (42 bp):
TATATATATATGTAGATATACATATAGATATACATATGTATA
Found at i:123329 original size:30 final size:30
Alignment explanation
Indices: 123134--123329 Score: 211
Period size: 30 Copynumber: 6.7 Consensus size: 30
123124 TATATACATG
** *
123134 TATATATACATATAGATATACATATGTATA
1 TATATATATGTATAGATATACATATGTAGA
* * * *
123164 TATATATATATGTAGATATACAAATGTATA
1 TATATATATGTATAGATATACATATGTAGA
123194 TATATATATG--TAGATATACATATGTAGA
1 TATATATATGTATAGATATACATATGTAGA
* * * *
123222 TATACAAATGTATATATATATATATGTAGA
1 TATATATATGTATAGATATACATATGTAGA
* * *
123252 TATACATATGTAT--ATATATATATGTATA
1 TATATATATGTATAGATATACATATGTAGA
* *
123280 TATATATATATGTAGATATACATATGTAGA
1 TATATATATGTATAGATATACATATGTAGA
*
123310 TATATATATGTATATATATA
1 TATATATATGTATAGATATA
123330 TAAAGAGGGG
Statistics
Matches: 142, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
28 48 0.34
30 94 0.66
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (30 bp):
TATATATATGTATAGATATACATATGTAGA
Found at i:124357 original size:20 final size:20
Alignment explanation
Indices: 124309--124360 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
124299 AATATATATC
* *
124309 TTTTCATCCAACAAATTCAT
1 TTTTCATCTAACAAATGCAT
*
124329 TACTTCATCTAACAAATGCAT
1 T-TTTCATCTAACAAATGCAT
124350 TTTTCATCTAA
1 TTTTCATCTAA
124361 ATGATGGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (20 bp):
TTTTCATCTAACAAATGCAT
Found at i:126492 original size:20 final size:19
Alignment explanation
Indices: 126446--126502 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
126436 TTATATCGAT
*
126446 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
126465 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
126484 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
126503 AAATGGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:126589 original size:33 final size:33
Alignment explanation
Indices: 126531--126599 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
126521 CTACCACTGT
* *
126531 TTGTATCGATACATGGTACAATGTATCGATATA
1 TTGTATCGATACATGATACAATGTATCGATACA
* *
126564 TTGTATCGATACATGATGA-ATTGTATTGATACA
1 TTGTATCGATACATGAT-ACAATGTATCGATACA
126597 TTG
1 TTG
126600 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCGATACA
Found at i:132687 original size:13 final size:13
Alignment explanation
Indices: 132666--132706 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
132656 TCGATACAAT
*
132666 ATTCCTTGTATCG
1 ATTCATTGTATCG
132679 ATTCATTGTATCG
1 ATTCATTGTATCG
*
132692 ATACATTGTATCG
1 ATTCATTGTATCG
132705 AT
1 AT
132707 ACATGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (13 bp):
ATTCATTGTATCG
Found at i:132707 original size:13 final size:13
Alignment explanation
Indices: 132671--132710 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
132661 ACAATATTCC
*
132671 TTGTATCGATTCA
1 TTGTATCGATACA
132684 TTGTATCGATACA
1 TTGTATCGATACA
132697 TTGTATCGATACA
1 TTGTATCGATACA
132710 T
1 T
132711 GGGTTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:135168 original size:13 final size:13
Alignment explanation
Indices: 135150--135174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135140 CATTATGTTT
135150 TGTATCGATACAA
1 TGTATCGATACAA
135163 TGTATCGATACA
1 TGTATCGATACA
135175 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.