Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2559
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: 58579
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4377 original size:52 final size:52
Alignment explanation
Indices: 4299--4425 Score: 209
Period size: 52 Copynumber: 2.4 Consensus size: 52
4289 CGAAATATGA
* * *
4299 AAATTTGCCTGCATGTATTGATACATTTCATAGTGTGTCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
4351 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
4403 AAATTTGCTTGCATGTATCGATA
1 AAATTTGCCTGCATGTATCGATA
4426 TAAAGATCAG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:4438 original size:52 final size:52
Alignment explanation
Indices: 4299--4447 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 52
4289 CGAAATATGA
* ** * *
4299 AAATTTGCCTGCATGTATTGATACATTTCATAGTGTGTCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* **
4351 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* * *
4403 AAATTTGCTTGCATGTATCGATATA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATAACAT-AGTGTATCGATACA
4448 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
Found at i:4454 original size:13 final size:13
Alignment explanation
Indices: 4436--4494 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
4426 TAAAGATCAG
4436 TGTATCGATACAA
1 TGTATCGATACAA
4449 TGTATCGATAC-A
1 TGTATCGATACAA
4461 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
4470 TGTATCGATACAA
1 TGTATCGATACAA
4483 TGTATCGATACA
1 TGTATCGATACA
4495 TTTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4479 original size:34 final size:34
Alignment explanation
Indices: 4436--4515 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
4426 TAAAGATCAG
4436 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
4470 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
4504 TGTATCGATACA
1 TGTATCGATACA
4516 TTTTCTTGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Found at i:6781 original size:21 final size:21
Alignment explanation
Indices: 6752--6792 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6742 AAAGGTCAAA
*
6752 ACCCTAGAAAGTATCGATACAG
1 ACCCTAG-AAGTATCAATACAG
6774 ACCC-AGAAGTATCAATACA
1 ACCCTAGAAGTATCAATACA
6793 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 2 0.11
22 4 0.22
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (21 bp):
ACCCTAGAAGTATCAATACAG
Found at i:7134 original size:34 final size:35
Alignment explanation
Indices: 7096--7168 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
7086 ATTTTCTACA
*
7096 TTTCAAAGAGCTTTTGTA-TTTTTTGTTG-TTATTC
1 TTTCAAAGAGCATTTGTATTTTTTTG-TGCTTATTC
**
7130 TTTCAAAGCTCATTTGTATTTTTTTGTGCTTATTC
1 TTTCAAAGAGCATTTGTATTTTTTTGTGCTTATTC
7165 TTTC
1 TTTC
7169 CACAAACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 17 0.50
35 17 0.50
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (35 bp):
TTTCAAAGAGCATTTGTATTTTTTTGTGCTTATTC
Found at i:14221 original size:28 final size:29
Alignment explanation
Indices: 14181--14251 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 29
14171 ATTTTTTTAT
14181 AAAAAGGGGAGAT-TATTTT-AGAAATAA-
1 AAAAAGGGGAGATAT-TTTTGAGAAATAAC
14208 AAAAAGGGAGAGATATTTTTGAGAAATAAC
1 AAAAAGGG-GAGATATTTTTGAGAAATAAC
14238 AAAAAAAGGGGAGA
1 --AAAAAGGGGAGA
14252 ATTGTTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
27 8 0.21
28 9 0.24
29 9 0.24
31 4 0.11
32 8 0.21
ACGTcount: A:0.54, C:0.01, G:0.25, T:0.20
Consensus pattern (29 bp):
AAAAAGGGGAGATATTTTTGAGAAATAAC
Found at i:14224 original size:27 final size:30
Alignment explanation
Indices: 14181--14251 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 30
14171 ATTTTTTTAT
14181 AAAAAGGGGAGATTA-TTTT-AGAAATAA-
1 AAAAAGGGGAGATTATTTTTGAGAAATAAC
14208 AAAAAGGGAGAGA-TATTTTTGAGAAATAAC
1 AAAAAGGG-GAGATTATTTTTGAGAAATAAC
14238 AAAAAAAGGGGAGA
1 --AAAAAGGGGAGA
14252 ATTGTTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
27 10 0.26
28 8 0.21
29 8 0.21
31 4 0.11
32 8 0.21
ACGTcount: A:0.54, C:0.01, G:0.25, T:0.20
Consensus pattern (30 bp):
AAAAAGGGGAGATTATTTTTGAGAAATAAC
Found at i:19608 original size:20 final size:20
Alignment explanation
Indices: 19572--19618 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19562 GATCAAATTA
* * *
19572 AGTCAAATGTTATCAACTTC
1 AGTCAAATGTGACCAACATC
*
19592 AGTCAAATGTGACCAACATG
1 AGTCAAATGTGACCAACATC
19612 AGTCAAA
1 AGTCAAA
19619 CTCGGGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (20 bp):
AGTCAAATGTGACCAACATC
Found at i:20201 original size:41 final size:43
Alignment explanation
Indices: 20156--20247 Score: 120
Period size: 41 Copynumber: 2.2 Consensus size: 43
20146 CTTCCATATC
* *
20156 TGAAATTTTTTATAT-TGAATC-TTCAATTAAACTTTTACC-CA
1 TGAAATTTTTTAAATAAG-ATCTTTCAATTAAACTTTTACCGCA
20197 TGAAA-TTTTTAAATAAGATCTTTCAATTAAACTTTTACCGCA
1 TGAAATTTTTTAAATAAGATCTTTCAATTAAACTTTTACCGCA
*
20239 TAAAATTTT
1 TGAAATTTT
20248 CAATATAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
40 11 0.25
41 24 0.55
42 6 0.14
43 3 0.07
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (43 bp):
TGAAATTTTTTAAATAAGATCTTTCAATTAAACTTTTACCGCA
Found at i:20371 original size:26 final size:27
Alignment explanation
Indices: 20319--20377 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
20309 CAATATAAAA
* *
20319 AATTCTCAACTAAACTTTTACATATAG
1 AATTTTCAACTAAACTTTTACACATAG
* *
20346 AGTTTTCAATTAAA-TTTTACACATAG
1 AATTTTCAACTAAACTTTTACACATAG
20372 AATTTT
1 AATTTT
20378 AGTAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (27 bp):
AATTTTCAACTAAACTTTTACACATAG
Found at i:20910 original size:8 final size:7
Alignment explanation
Indices: 20899--20963 Score: 62
Period size: 7 Copynumber: 8.9 Consensus size: 7
20889 GATCTTGAGA
20899 AAAAAATG
1 AAAAAA-G
20907 AAAAAA-
1 AAAAAAG
20913 AAAAAAG
1 AAAAAAG
20920 AAAAATAG
1 AAAAA-AG
*
20928 AGAAAAAT
1 A-AAAAAG
20936 AAAGAGAA-
1 AAA-A-AAG
20944 AAAAAAG
1 AAAAAAG
20951 AAAAAAG
1 AAAAAAG
20958 AAAAAA
1 AAAAAA
20964 AGTTCTTGCA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
6 8 0.16
7 21 0.42
8 15 0.30
9 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:20916 original size:13 final size:13
Alignment explanation
Indices: 20898--20963 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 13
20888 TGATCTTGAG
*
20898 AAAAAAATGAAAA
1 AAAAAAAAGAAAA
20911 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
*
20924 ATAGAGAAAAATAAAGA
1 A-A-A-AAAAAGAAA-A
20941 GAAAAAAAAGAAAA
1 -AAAAAAAAGAAAA
20955 AAGAAAAAA
1 AA-AAAAAA
20964 AGTTCTTGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 15 0.34
14 8 0.18
15 9 0.20
16 9 0.20
17 2 0.05
18 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:20964 original size:10 final size:10
Alignment explanation
Indices: 20896--20956 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
20886 TTTGATCTTG
20896 AGAAAAAAATGA
1 AGAAAAAAA--A
*
20908 AAAAAAAAAA
1 AGAAAAAAAA
* *
20918 AGAAAAATAG
1 AGAAAAAAAA
*
20928 AGAAAAATAA
1 AGAAAAAAAA
20938 AGAGAAAAAAA
1 AGA-AAAAAAA
20949 AGAAAAAA
1 AGAAAAAA
20957 GAAAAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
10 25 0.60
11 9 0.21
12 8 0.19
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:21700 original size:36 final size:35
Alignment explanation
Indices: 21635--21732 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 35
21625 CACTGTTACT
* *
21635 TCATTTCATTTTATTTACTTTATGCTCATATTAAA
1 TCATTTTATTTTATTTACTTTATGTTCATATTAAA
* **
21670 TCATTTTATTTTATTCACTTTTATGTTCATATTATT
1 TCATTTTATTTTATTTAC-TTTATGTTCATATTAAA
*
21706 TTATTTTTATTTTATTTACTTTATGTT
1 TCA-TTTTATTTTATTTACTTTATGTT
21733 TTCTATTTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 16 0.30
36 24 0.44
37 14 0.26
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.63
Consensus pattern (35 bp):
TCATTTTATTTTATTTACTTTATGTTCATATTAAA
Found at i:21758 original size:17 final size:17
Alignment explanation
Indices: 21717--21764 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
21707 TATTTTTATT
** *
21717 TTATTTACTTTATGTTT
1 TTATTTACTTTACATTG
21734 TCTATTTACTTTACATTG
1 T-TATTTACTTTACATTG
21752 TTATTTACTTTAC
1 TTATTTACTTTAC
21765 CTTATTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.62
Consensus pattern (17 bp):
TTATTTACTTTACATTG
Found at i:22756 original size:19 final size:19
Alignment explanation
Indices: 22732--22768 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22722 TGATGCGTAC
22732 TGATACCTTGGTACTAAAT
1 TGATACCTTGGTACTAAAT
*
22751 TGATACCTTGGTGCTAAA
1 TGATACCTTGGTACTAAA
22769 ATTGGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (19 bp):
TGATACCTTGGTACTAAAT
Found at i:24534 original size:11 final size:9
Alignment explanation
Indices: 24505--24544 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
24495 ACTTTAAAGA
*
24505 AATTTAAAT
1 AATTTATAT
24514 AATTTATAT
1 AATTTATAT
24523 ACATTATATAT
1 A-ATT-TATAT
24534 AATTTATAT
1 AATTTATAT
24543 AA
1 AA
24545 AAAATACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 16 0.57
10 6 0.21
11 6 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTTATAT
Found at i:28869 original size:21 final size:20
Alignment explanation
Indices: 28830--28874 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28820 GTTTGCAAAG
*
28830 ACAAGTGTCAATACTTTAGGT
1 ACAAGTATCAATACTTTA-GT
28851 ACAAGTATCAATA-TCTTAGT
1 ACAAGTATCAATACT-TTAGT
28871 ACAA
1 ACAA
28875 AATTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (20 bp):
ACAAGTATCAATACTTTAGT
Found at i:35246 original size:20 final size:20
Alignment explanation
Indices: 35223--35262 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35213 ATATTTTATT
35223 ATATTATA-ATTATATTTAAA
1 ATATTATATATT-TATTTAAA
*
35243 ATATTTTATATTTATTTAAA
1 ATATTATATATTTATTTAAA
35263 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTATATATTTATTTAAA
Found at i:35707 original size:44 final size:44
Alignment explanation
Indices: 35644--35733 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
35634 AAAATGGAGT
35644 TGGGTCTTATCATTGAATCGAAATCAATTATTGATGTACCTTGG
1 TGGGTCTTATCATTGAATCGAAATCAATTATTGATGTACCTTGG
35688 TGGGTCTTATCATTGAATCGAAATCAATTATTGATGTACCTTGG
1 TGGGTCTTATCATTGAATCGAAATCAATTATTGATGTACCTTGG
35732 TG
1 TG
35734 TAGAAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (44 bp):
TGGGTCTTATCATTGAATCGAAATCAATTATTGATGTACCTTGG
Found at i:36408 original size:13 final size:13
Alignment explanation
Indices: 36390--36414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36380 TTCAATGATT
36390 TGTATCGATACAA
1 TGTATCGATACAA
36403 TGTATCGATACA
1 TGTATCGATACA
36415 TAAGTGTTGT
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:36563 original size:52 final size:52
Alignment explanation
Indices: 36519--36647 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
36509 CACTGATCTT
36519 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
36571 TGTATCGATACATACAGGCAAATTTGCTCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
36623 TGTATCGATACATGGAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
36648 TCATATTCGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:43923 original size:31 final size:31
Alignment explanation
Indices: 43888--44112 Score: 190
Period size: 31 Copynumber: 7.1 Consensus size: 31
43878 TTCACATCTA
* *
43888 TTTTCTCCAAAGTCCACGACTCAGTGGCATT
1 TTTTCTCCAAAGTCCACAACTCAGTGGCATC
43919 TTTTCTCCAAAGTCCACAACTCAGTGGCAATC
1 TTTTCTCCAAAGTCCACAACTCAGTGGC-ATC
* *
43951 TCTTT-T-CAAAGTCCACGACTTAGTGGCATC
1 T-TTTCTCCAAAGTCCACAACTCAGTGGCATC
** *
43981 TTTTCTTTAAAGTCCACAACTCCGTGGCAACTC
1 TTTTCTCCAAAGTCCACAACTCAGTGGC-A-TC
* *
44014 TTTCCTTCAAAGTCCACAACTCAGTGGCATCCC
1 TTTTCTCCAAAGTCCACAACTCAGTGGCAT--C
* * *
44047 TTTT-TCCTGTAAGTCTACAATTCAGTGGCATC
1 TTTTCTCC--AAAGTCCACAACTCAGTGGCATC
* * * *
44079 TCTTT-T-CTAAGTCCACGACTCCGTGGCACC
1 T-TTTCTCCAAAGTCCACAACTCAGTGGCATC
44109 TTTT
1 TTTT
44113 TCTTTTTAAA
Statistics
Matches: 162, Mismatches: 21, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
29 6 0.04
30 24 0.15
31 64 0.40
32 11 0.07
33 38 0.23
34 19 0.12
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (31 bp):
TTTTCTCCAAAGTCCACAACTCAGTGGCATC
Found at i:43993 original size:62 final size:63
Alignment explanation
Indices: 43895--44133 Score: 263
Period size: 62 Copynumber: 3.7 Consensus size: 63
43885 CTATTTTCTC
**
43895 CAAAGTCCACGACTCAGTGGCAT-TTTTTCTCCAAAGTCCACAACTCAGTGGCAATCTCTTTT
1 CAAAGTCCACGACTCAGTGGCATCTTTTTCTTTAAAGTCCACAACTCAGTGGCAATCTCTTTT
* *
43957 CAAAGTCCACGACTTAGTGGCATC-TTTTCTTTAAAGTCCACAACTCCGTGGCAA-CTCTTTCCT
1 CAAAGTCCACGACTCAGTGGCATCTTTTTCTTTAAAGTCCACAACTCAGTGGCAATCTC-TT--T
44020 T
63 T
* * * *
44021 CAAAGTCCACAACTCAGTGGCATCCCTTTTTCCTGT-AAGTCTACAATTCAGTGGC-ATCTCTTT
1 CAAAGTCCACGACTCAGTGGCAT--CTTTTT-CTTTAAAGTCCACAACTCAGTGGCAATCTCTTT
44084 T
63 T
* * * *
44085 CTAAGTCCACGACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTC
1 CAAAGTCCACGACTCAGTGGCATCTTTTTC--TTTAAAGTCCACAACTC
44134 CGCGGCACTC
Statistics
Matches: 147, Mismatches: 18, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
61 4 0.03
62 57 0.39
63 2 0.01
64 54 0.37
66 4 0.03
67 23 0.16
68 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (63 bp):
CAAAGTCCACGACTCAGTGGCATCTTTTTCTTTAAAGTCCACAACTCAGTGGCAATCTCTTTT
Found at i:44149 original size:64 final size:64
Alignment explanation
Indices: 43895--44149 Score: 247
Period size: 64 Copynumber: 4.0 Consensus size: 64
43885 CTATTTTCTC
* ** *
43895 CAAAGTCCACGACTCAGTGGCA--TTTTTTCTCCAAAGTCCACAACTCAGTGGCAATCTCTTTT
1 CAAAGTCCACGACTCAGTGGCACCTTTTTCCTTTAAAGTCCACAACTCAGTGGCACTCTCTTTT
* * *
43957 CAAAGTCCACGACTTAGTGGCATC-TTTT-CTTTAAAGTCCACAACTCCGTGGCAACTCT-TTCC
1 CAAAGTCCACGACTCAGTGGCACCTTTTTCCTTTAAAGTCCACAACTCAGTGGC-ACTCTCTT--
44019 TT
63 TT
* * * *
44021 CAAAGTCCACAACTCAGTGGCATCCCTTTTTCCTGT-AAGTCTACAATTCAGTGGCA-TCTCTTT
1 CAAAGTCCACGACTCAGTGGCA--CCTTTTTCCTTTAAAGTCCACAACTCAGTGGCACTCTCTTT
44084 T
64 T
* * * * * *
44085 CTAAGTCCACGACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGCGGCACTCT-TTTT
1 CAAAGTCCACGACTCAGTGGCACCTTTTTC-CTTTAAAGTCCACAACTCAGTGGCACTCTCTTTT
44149 C
1 C
44150 CCTTTTAAGT
Statistics
Matches: 158, Mismatches: 22, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
62 52 0.33
63 10 0.06
64 63 0.40
65 6 0.04
66 4 0.03
67 20 0.13
68 3 0.02
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.33
Consensus pattern (64 bp):
CAAAGTCCACGACTCAGTGGCACCTTTTTCCTTTAAAGTCCACAACTCAGTGGCACTCTCTTTT
Found at i:44164 original size:35 final size:34
Alignment explanation
Indices: 43959--44182 Score: 166
Period size: 34 Copynumber: 6.8 Consensus size: 34
43949 TCTCTTTTCA
* ** *
43959 AAGTCCACGACTTAGTGGCA-TC-TTTT-CTTTA
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
**
43990 AAGTCCACAACTCCGTGGCAACTC--TTTCCTTCA
1 AAGTCCACAACTCCGTGGC-ACTCTTTTTCCTTTT
* * *
44023 AAGTCCACAACTCAGTGGCATCCCTTTTTCC-TGT
1 AAGTCCACAACTCCGTGGCA-CTCTTTTTCCTTTT
* * *
44057 AAGTCTACAATTCAGTGGCA-TCTCTTTT-C---T
1 AAGTCCACAACTCCGTGGCACTCT-TTTTCCTTTT
* *
44087 AAGTCCACGACTCCGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
44120 AAAGCCCACAACTCCGCGGCACTCTTTTTCCCTTTT
1 -AAGTCCACAACTCCGTGGCACTCTTTTT-CCTTTT
*
44156 AAGTCCACAACTCCATGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTT
44183 AAGTCCACAA
Statistics
Matches: 155, Mismatches: 23, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
29 4 0.03
30 19 0.12
31 16 0.10
32 8 0.05
33 31 0.20
34 37 0.24
35 35 0.23
36 5 0.03
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:44181 original size:27 final size:27
Alignment explanation
Indices: 44151--44234 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
44141 CTCTTTTTCC
44151 CTTTTAAGTCCACAACTCCATGGCACT
1 CTTTTAAGTCCACAACTCCATGGCACT
*
44178 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCATGGCACT
* * *
44205 CTTTTAAGTCCATAATTCCGTGGCA-T
1 CTTTTAAGTCCACAACTCCATGGCACT
44231 CTTT
1 CTTT
44235 CACCTTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
26 4 0.08
27 48 0.92
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCATGGCACT
Found at i:46661 original size:9 final size:9
Alignment explanation
Indices: 46647--46673 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
46637 AAGTGACTTC
46647 AAATCATCA
1 AAATCATCA
46656 AAATCATCA
1 AAATCATCA
46665 AAATCATCA
1 AAATCATCA
46674 CAATAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
AAATCATCA
Found at i:47527 original size:52 final size:52
Alignment explanation
Indices: 47457--47577 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
47447 GAAAATTTAT
*
47457 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
47509 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
47561 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
47578 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:47590 original size:52 final size:51
Alignment explanation
Indices: 47457--47597 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
47447 GAAAATTTAT
47457 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
47509 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
47561 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
47598 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:47604 original size:13 final size:13
Alignment explanation
Indices: 47586--47610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47576 CAAAGATCAG
47586 TGTATCGATACAA
1 TGTATCGATACAA
47599 TGTATCGATACA
1 TGTATCGATACA
47611 TTTGAATAAT
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:47691 original size:13 final size:13
Alignment explanation
Indices: 47673--47697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47663 CAAAAAAATA
47673 TGTATCGATACAT
1 TGTATCGATACAT
47686 TGTATCGATACA
1 TGTATCGATACA
47698 ACACTCTATG
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:48647 original size:55 final size:52
Alignment explanation
Indices: 48547--49148 Score: 358
Period size: 43 Copynumber: 12.7 Consensus size: 52
48537 GAAAAGTGAT
* * * * * * *
48547 AAAGATGCCAATATGTTGATTCACGGCCAACGATATT-AGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAGATG-G-A
* *
48601 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
48654 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
48697 AAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
48746 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
48789 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * * * *
48839 -AAGATGCCAAAATGCTGATACAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
48881 AAAGGTGCCAATGTGCTGATTCAAGGCC-GCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
48930 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
48972 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
49022 -AAGATGCCAATATGCTGATACAAGGCCAG-TGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCT-ACATTGAACTTAAAGATGGA
*
49064 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
49114 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACAT
49149 CAATATGTTG
Statistics
Matches: 452, Mismatches: 52, Indels: 93
0.76 0.09 0.16
Matches are distributed among these distances:
42 10 0.02
43 174 0.38
44 5 0.01
46 1 0.00
48 32 0.07
49 150 0.33
51 1 0.00
52 32 0.07
53 6 0.01
54 5 0.01
55 35 0.08
56 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:48715 original size:43 final size:43
Alignment explanation
Indices: 48654--50337 Score: 1239
Period size: 43 Copynumber: 36.8 Consensus size: 43
48644 TAAAGATGGA
*
48654 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
48697 AAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
48740 AAAGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
48789 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * * *
48832 AAAGATGAAGATGCCAAAATGCTGATACAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
48881 AAAGGTGCCAATGTGCTGATTCAAGGCC-GCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
48923 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
48972 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
49015 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAG-TGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCT-ACATTGGACTT
49064 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
49107 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATCAATATGTTGA-TT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCT--A-C-AT-TG--GACTT
* * * * * * * *
49162 -CACG-GCC-A-ACGAT-ATT--AGG-C--TTAAAGATGAGA--A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACA-TTG-GACTT
* * *
49195 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
*
49245 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
49291 AAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
49334 AAAGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
49383 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
49426 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
49475 AAAGGTGCCAATGTGCTGATTCAAGGCC-GCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
49517 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
49566 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
49609 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
49658 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
49701 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATCAATATGTTGA-TT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCT--A-C-AT-TG--GACTT
* * * * * * * *
49756 -CACG-GCC-A-ACGAT-ATT--AGG-C--TTAAAGATGAGA--A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACA-TTG-GACTT
* * *
49789 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
*
49839 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
49885 AAAGGTGTCAATGTGCTGATTCAGGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
49928 AAAGAAAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
49977 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
50020 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
50069 AAAGGTACCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
***
50112 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGGTATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
50161 AAAGGTGCCAATGTGATGATTCAAGGCCAGCTACATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
50204 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
50253 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
50296 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACAT
50338 CAATATGTTG
Statistics
Matches: 1322, Mismatches: 165, Indels: 302
0.74 0.09 0.17
Matches are distributed among these distances:
34 8 0.01
35 6 0.00
36 4 0.00
37 4 0.00
38 4 0.00
39 8 0.01
41 8 0.01
42 34 0.03
43 531 0.40
44 29 0.02
45 13 0.01
46 18 0.01
47 16 0.01
48 75 0.06
49 468 0.35
51 4 0.00
52 66 0.05
53 14 0.01
54 4 0.00
55 4 0.00
56 4 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:48786 original size:92 final size:92
Alignment explanation
Indices: 48601--50332 Score: 1581
Period size: 92 Copynumber: 18.9 Consensus size: 92
48591 AAGATGAGAA
* *
48601 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
*
48666 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
48697 AAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
48762 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
48789 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAAAATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
48854 TGATACAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
48881 AAAGGTGCCAATGTGCTGATTCAAGGCC-GCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
48945 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
48972 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* *
49037 TGATACAAGGCCAGTGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
49064 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* *
49129 TGAGTCAAGGCCAGCTACATCAATATGTTGA-TT
66 TGATTCAAGGCCAGC--GAT--AT-TG--GACTT
* * * * * * * * * *
49162 -CACG-GCCAA--CGAT-ATT--AGG-C--TTA-A--AGA--T-GAGAAAAAGGATGTCAATGTG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGG-TGCCAATATG
* * *
49211 CTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
65 CTGATTCAAGGCCAGCGATATTGGAC-T-----T
* * * *
49245 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGTCAATG
1 ---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
* * *
49304 TGCTGATTCAAGGCTAGCTACATTGGACTT
63 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
49334 AAAGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCA
1 ------AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCA
* * *
49393 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
49426 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCA
1 -AA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCA
* * *
49485 ATGTGCTGATTCAAGGCC-GCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
49517 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCA
* * *
49576 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
49609 AAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCA
1 -AA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCA
* * *
49668 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *** ** *
49701 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACA-T-CAATATGTTGATTCACG-GCC
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT-TAAAGATAAAGGTGCC
* * * * * *
49763 -A-ACGAT-ATT--AGGCTTA--AAGA-TGAGA--A
59 AATATGCTGATTCAAGGC-CAGCGATATTG-GACTT
* *
49789 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
*
49854 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
49885 AAAGGTGTCAATGTGCTGATTCAGGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
49950 TAATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
49977 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
50042 TGATACAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
50069 AAAGGTACCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
50134 TGATTCAAGGCCAGCGGTATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * * *
50161 AAAGGTGCCAATGTGATGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
50226 TGATACAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
50253 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
50318 TGAGTCAAGGCCAGC
66 TGATTCAAGGCCAGC
50333 TACATCAATA
Statistics
Matches: 1433, Mismatches: 120, Indels: 170
0.83 0.07 0.10
Matches are distributed among these distances:
76 1 0.00
78 3 0.00
79 2 0.00
81 1 0.00
82 11 0.01
83 54 0.04
84 6 0.00
85 4 0.00
87 9 0.01
88 12 0.01
89 7 0.00
90 11 0.01
91 183 0.13
92 934 0.65
93 14 0.01
94 14 0.01
95 122 0.09
96 29 0.02
97 9 0.01
98 2 0.00
99 4 0.00
100 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:49367 original size:319 final size:314
Alignment explanation
Indices: 48881--49462 Score: 986
Period size: 319 Copynumber: 1.8 Consensus size: 314
48871 TATTGGACTT
*
48881 AAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCT
48946 GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
66 GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
** *
49011 ACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGTGATATTGGACTTAAAGGTGCCAAT
131 ACTTAAAGAAAAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
* *
49076 ATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT-CAAGGC
196 ATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGA-TACAAGGC
49140 CAGCTACATCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAA
260 CAGCTACATCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAA
*
49195 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCC-GCTACATTGAACTTAAAGAT-G--AAGGTGCCAAT
* * *
49260 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTAC
61 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
* *
49325 ATTGGACTTAAAGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
126 ATTGGACTTAAAGAAAAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTG
*
49390 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACA
191 CCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACA
49455 AGGCCAGC
256 AGGCCAGC
49463 GATATTGGAC
Statistics
Matches: 249, Mismatches: 13, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
314 5 0.02
315 22 0.09
316 19 0.08
317 1 0.00
318 1 0.00
319 201 0.81
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (314 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
ACTTAAAGAAAAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
ATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCC
AGCTACATCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAA
Found at i:49568 original size:594 final size:594
Alignment explanation
Indices: 48555--50482 Score: 3673
Period size: 594 Copynumber: 3.2 Consensus size: 594
48545 ATAAAGATGC
48555 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
1 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
48620 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
66 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
48685 TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAG
131 TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAG
48750 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
196 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
*
48815 CCAGCTACATTGGACTTAAAGATGAAGATGCCAAAATGCTGATACAAGGCCAGCGATATTGGACT
261 CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACT
48880 TAAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
326 TAAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
48945 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
391 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
*
49010 GACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGTGATATTGGACTTAAAGGTGCCAA
456 GACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAA
*
49075 TATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGC
521 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGC
49140 CAGCTACAT
586 CAGCTACAT
49149 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
1 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
49214 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
66 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
49279 TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAG
131 TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAG
49344 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
196 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
49409 CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACT
261 CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACT
49474 TAAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
326 TAAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
49539 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
391 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
49604 GACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAA
456 GACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAA
49669 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGC
521 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGC
49734 CAGCTACAT
586 CAGCTACAT
49743 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
1 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
49808 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
66 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
* *
49873 TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAGGGCCAGCTACATTGGACTTAAAGAAAAAG
131 TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAG
*
49938 GTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
196 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
50003 CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACT
261 CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACT
* *
50068 TAAAGGTACCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
326 TAAAGGTGCCAATGTGCTGATTCAAGGCC-GCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
50133 CTGATTCAAGGCCAGCGGTATTGGACTTAAAGGTGCCAATGTGATGATTCAAGGCCAGCTACATT
390 CTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
*
50198 GGATTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCA
455 GGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCA
50263 ATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGG
520 ATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGG
50328 CCAGCTACAT
585 CCAGCTACAT
50338 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
1 CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
* * * *
50403 ATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCTAATAAGCTGATTCAAGGCCAGC
66 ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
*
50465 TATATTGGGCTTAGAAGG
131 TATATTGGACTTA-AAGG
50483 GTTGCCACCG
Statistics
Matches: 1316, Mismatches: 16, Indels: 5
0.98 0.01 0.00
Matches are distributed among these distances:
592 41 0.03
593 4 0.00
594 940 0.71
595 331 0.25
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (594 bp):
CAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
ATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
TATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAAAAG
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACT
TAAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
GACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAA
TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGC
CAGCTACAT
Found at i:49916 original size:319 final size:314
Alignment explanation
Indices: 49475--50056 Score: 995
Period size: 319 Copynumber: 1.8 Consensus size: 314
49465 TATTGGACTT
*
49475 AAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCT
49540 GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
66 GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
** *
49605 ACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
131 ACTTAAAGAAAAAGATGCCAATATGCTAATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
* *
49670 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT-CAAGGC
196 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGA-TACAAGGC
49734 CAGCTACATCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAA
260 CAGCTACATCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAA
*
49789 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCC-GCTACATTGAACTTAAAGAT-G--AAGGTGCCAAT
* * *
49854 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTCAATGTGCTGATTCAGGGCCAGCTAC
61 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
* *
49919 ATTGGACTTAAAGAAAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGTG
126 ATTGGACTTAAAGAAAAAGATGCCAATATGCTAATACAAGGCCAGCGATATTGGACTTAAAGGTG
49984 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACA
191 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACA
50049 AGGCCAGC
256 AGGCCAGC
50057 GATATTGGAC
Statistics
Matches: 250, Mismatches: 12, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
314 5 0.02
315 22 0.09
316 19 0.08
317 1 0.00
318 1 0.00
319 202 0.81
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (314 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
ACTTAAAGAAAAAGATGCCAATATGCTAATACAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATACAAGGCC
AGCTACATCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAA
Found at i:50519 original size:32 final size:32
Alignment explanation
Indices: 50470--50573 Score: 169
Period size: 32 Copynumber: 3.3 Consensus size: 32
50460 CCAGCTATAT
50470 TGGGC-TT-AGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
*
50500 TGGGCTTT-AGAGCGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAGA-AGGGTTGCCACCGACTTGTG
50532 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
50564 TGGGCTTTGA
1 TGGGCTTTGA
50574 AAAGAAGGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
30 5 0.07
31 5 0.07
32 56 0.81
33 3 0.04
ACGTcount: A:0.14, C:0.19, G:0.38, T:0.29
Consensus pattern (32 bp):
TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
Found at i:50624 original size:34 final size:34
Alignment explanation
Indices: 50581--51151 Score: 289
Period size: 34 Copynumber: 17.8 Consensus size: 34
50571 TGAAAAGAAG
50581 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
*
50615 GTGCCACGGAGTTGTGGGC-TT-AAACG-----G-
1 GTGCCACGGAGTTGTGGACTTTGAAA-GAAAAAGA
* *
50642 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* *
50676 GTGCCACGGTGTTGTGGGC-TT-AAACG-----G-
1 GTGCCACGGAGTTGTGGACTTTGAAA-GAAAAAGA
* *
50703 GTGCCACGGAGTTGTGGACTTAG-AAGGAAAAGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* * * *
50736 GTGCCACGTAGTTGTGGGCTTTG-CAGAAAAGGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* * ** ** * *
50769 -TACTACTAAGTCATGGACTGTAAAAGGGAAAAAGA
1 GTGCCACGGAGTTGTGGACTTTGAAA--GAAAAAGA
*
50804 GTGCCACGGAGTTATGGACTTTGAAAAGAAAAAG-
1 GTGCCACGGAGTTGTGGACTTTG-AAAGAAAAAGA
* *
50838 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* *
50872 GTGCCACGGTGTTGTGGGC-TT-AAACG-----G-
1 GTGCCACGGAGTTGTGGACTTTGAAA-GAAAAAGA
* *
50899 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* * * *
50933 ATGCCACGGTGTTGTGGGCTTTAAAAAGAAAAAG-
1 GTGCCACGGAGTTGTGGACTTT-GAAAGAAAAAGA
* * * *
50967 GTTGCCATGGAATTGTGGGCTTT------AAAAGG
1 G-TGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* * *
50996 GTGCCATGGAGTTGTGGA-TTTAAAAGGAACAAG-
1 GTGCCACGGAGTTGTGGACTTTGAAA-GAAAAAGA
*
51029 GTGCCACGGAGTTGTGGGCTTTTG-AAGAAAAA-A
1 GTGCCACGGAGTTGTGGAC-TTTGAAAGAAAAAGA
* * *
51062 -TGCCACTGAGTCGTGGACTTTG--AGACAAA-A
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* * * *
51092 -TGCCACTGAGTCGTGGATTTTG-AAGAAAAGGA
1 GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
* **
51124 -TGCCACTGAGTCATGGACTTTGAGAAGA
1 GTGCCACGGAGTTGTGGACTTTGA-AAGA
51152 GATTGCCATT
Statistics
Matches: 415, Mismatches: 72, Indels: 100
0.71 0.12 0.17
Matches are distributed among these distances:
27 56 0.13
28 30 0.07
29 5 0.01
30 28 0.07
31 9 0.02
32 57 0.14
33 67 0.16
34 101 0.24
35 44 0.11
36 15 0.04
37 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.22
Consensus pattern (34 bp):
GTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGA
Found at i:50653 original size:27 final size:27
Alignment explanation
Indices: 50615--50724 Score: 121
Period size: 27 Copynumber: 3.8 Consensus size: 27
50605 AAGAAAAAGA
*
50615 GTGCCACGGAGTTGTGGGCTTAAACGG
1 GTGCCACGGAGTTGTGGACTTAAACGG
*
50642 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAG
1 GTGCCACGGAGTTGTGGACTTA-AACG-----G
* *
50675 AGTGCCACGGTGTTGTGGGCTTAAACGG
1 -GTGCCACGGAGTTGTGGACTTAAACGG
50703 GTGCCACGGAGTTGTGGACTTA
1 GTGCCACGGAGTTGTGGACTTA
50725 GAAGGAAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
27 41 0.59
28 4 0.06
33 4 0.06
34 20 0.29
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (27 bp):
GTGCCACGGAGTTGTGGACTTAAACGG
Found at i:50654 original size:61 final size:61
Alignment explanation
Indices: 50580--50953 Score: 410
Period size: 61 Copynumber: 5.9 Consensus size: 61
50570 TTGAAAAGAA
*
50580 GGTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
* *
50641 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGTGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
* * *
50702 GGTGCCACGGAGTTGTGGACTTAG-AAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTGCAGAAAA
1 GGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGC-TT----AAAC
50766 G
61 G
* * * ** ** * * *
50767 GATACTACTAAGTCATGGACTGTA-AAAGGGAAAAAGAGTGCCACGGAGTTATGGACTTTGAAAA
1 GGTGCCACGGAGTTGTGGACT-TAGAAA--GAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAC
50831 G
61 G
* *
50832 AAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGTGTTGTGGGCTTAAAC
1 -----GGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAC
50897 G
61 G
* * *
50898 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAATGCCACGGTGTTGTGGGCTT
1 GGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
50954 TAAAAAGAAA
Statistics
Matches: 266, Mismatches: 32, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
60 25 0.09
61 139 0.52
65 24 0.09
66 8 0.03
67 2 0.01
68 50 0.19
69 2 0.01
70 16 0.06
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (61 bp):
GGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
Found at i:51002 original size:28 final size:27
Alignment explanation
Indices: 50962--51022 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
50952 TTTAAAAAGA
* *
50962 AAAAGGTTGCCATGGAATTGTGGGCTTT
1 AAAAGGGTGCCATGGAATTGT-GGATTT
*
50990 AAAAGGGTGCCATGGAGTTGTGGATTT
1 AAAAGGGTGCCATGGAATTGTGGATTT
51017 AAAAGG
1 AAAAGG
51023 AACAAGGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.28
Consensus pattern (27 bp):
AAAAGGGTGCCATGGAATTGTGGATTT
Found at i:51046 original size:61 final size:63
Alignment explanation
Indices: 50934--51050 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 63
50924 GGAAAAAGAA
* * *
50934 TGCCACGGTGTTGTGGGCTTTAAAAAGAAAAAGGTTGCCATGGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGGATTTAAAAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGG
* * * *
50997 TGCCATGGAGTTGT-GGATTTAAAAGGAACAAGG-TGCCACGGAGTTGTGGGCTTT
1 TGCCACGGAGTTGTGGGATTTAAAAAGAAAAAGGTTGCCACGGAATTGTGGGCTTT
51051 TGAAGAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 19 0.40
62 16 0.34
63 12 0.26
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.27
Consensus pattern (63 bp):
TGCCACGGAGTTGTGGGATTTAAAAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGG
Found at i:51128 original size:62 final size:62
Alignment explanation
Indices: 51030--51170 Score: 178
Period size: 62 Copynumber: 2.3 Consensus size: 62
51020 AGGAACAAGG
* * * *
51030 TGCCACGGAGTTGTGGGCTTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGT-GGATTTTGAAGAAAAAATGCCACTGAGTCATGGACTTTGAGA-AGAGAA
* *
51092 TGCCACTGAGTCGTGGATTTTGAAGAAAAGGATGCCACTGAGTCATGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGATTTTGAAGAAAA-AATGCCACTGAGTCATGGACTTTGAGAAGAGAA
*
51155 TGCCATTGAGTCGTGG
1 TGCCACTGAGTCGTGG
51171 GCTTTGAGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 15 0.22
62 38 0.55
63 16 0.23
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGATTTTGAAGAAAAAATGCCACTGAGTCATGGACTTTGAGAAGAGAA
Found at i:51132 original size:32 final size:31
Alignment explanation
Indices: 51030--51170 Score: 144
Period size: 32 Copynumber: 4.5 Consensus size: 31
51020 AGGAACAAGG
* * * *
51030 TGCCACGGAGTTGTGGGCTTTTGAAGAAAAAA
1 TGCCACTGAGTCGT-GGATTTTGAAGAAAAGA
*
51062 TGCCACTGAGTCGTGGACTTTG-AGACAAA-A
1 TGCCACTGAGTCGTGGATTTTGAAGA-AAAGA
51092 TGCCACTGAGTCGTGGATTTTGAAGAAAAGGA
1 TGCCACTGAGTCGTGGATTTTGAAGAAAA-GA
* * *
51124 TGCCACTGAGTCATGGACTTTG-AGAAGAGA
1 TGCCACTGAGTCGTGGATTTTGAAGAAAAGA
*
51154 TTGCCATTGAGTCGTGG
1 -TGCCACTGAGTCGTGG
51171 GCTTTGAGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
30 30 0.32
31 31 0.33
32 33 0.35
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGATTTTGAAGAAAAGA
Found at i:51165 original size:31 final size:31
Alignment explanation
Indices: 51062--51186 Score: 148
Period size: 31 Copynumber: 4.0 Consensus size: 31
51052 GAAGAAAAAA
*
51062 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAT
* *
51092 TGCCACTGAGTCGTGGATTTTGAAGAAAAGGA-
1 TGCCACTGAGTCGTGGACTTTG-AGAAGA-GAT
*
51124 TGCCACTGAGTCATGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
* *
51155 TGCCATTGAGTCGTGGGCTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
51186 T
1 T
51187 TGAAGAATTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
30 24 0.29
31 38 0.46
32 20 0.24
33 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:51303 original size:8 final size:8
Alignment explanation
Indices: 51280--51325 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
51270 GATGCAAATA
51280 ATGATGTT
1 ATGATGTT
51288 ATTGATGTT
1 A-TGATGTT
51297 ATGATGTT
1 ATGATGTT
*
51305 ATGATGTC
1 ATGATGTT
*
51313 ATGATGTC
1 ATGATGTT
51321 ATGAT
1 ATGAT
51326 TACAACACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
8 28 0.78
9 8 0.22
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (8 bp):
ATGATGTT
Found at i:52185 original size:16 final size:16
Alignment explanation
Indices: 52166--52199 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52156 TTTTTGTTTG
*
52166 TGTTTTTTTTCTTTTT
1 TGTTTTCTTTCTTTTT
52182 TGTTTTCTTTCTTTTT
1 TGTTTTCTTTCTTTTT
52198 TG
1 TG
52200 GAAAAGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (16 bp):
TGTTTTCTTTCTTTTT
Found at i:52196 original size:22 final size:22
Alignment explanation
Indices: 52146--52197 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
52136 TTTTCCCTTT
** *
52146 TTTTTTTTGGTTTTTGTTTGTG
1 TTTTTTTTCTTTTTTGTTTGTC
52168 TTTTTTTTCTTTTTTGTTT-TC
1 TTTTTTTTCTTTTTTGTTTGTC
52189 TTTCTTTTT
1 TTT-TTTTT
52198 TGGAAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.83
Consensus pattern (22 bp):
TTTTTTTTCTTTTTTGTTTGTC
Found at i:58117 original size:52 final size:52
Alignment explanation
Indices: 58047--58167 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
58037 GAAAATTTAT
*
58047 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
58099 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
58151 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
58168 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:58180 original size:52 final size:51
Alignment explanation
Indices: 58047--58187 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
58037 GAAAATTTAT
58047 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* * *
58099 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
58151 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
58188 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:58194 original size:13 final size:13
Alignment explanation
Indices: 58176--58200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58166 CAAAGATCAG
58176 TGTATCGATACAA
1 TGTATCGATACAA
58189 TGTATCGATACA
1 TGTATCGATACA
58201 TTTGAATAAT
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:58280 original size:13 final size:13
Alignment explanation
Indices: 58262--58286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58252 ACAAAAAATA
58262 TGTATCGATACAT
1 TGTATCGATACAT
58275 TGTATCGATACA
1 TGTATCGATACA
58287 ACACTCTATG
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
Done.