Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:3874 original size:21 final size:22
Alignment explanation
Indices: 3848--3896 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
3838 ATTCATTTAA
3848 ATGAAAAT-ATGCA-TTGATTGG
1 ATGAAAATAATGCATTTG-TTGG
3869 ATG-AAATAATGCATTTGTTGG
1 ATGAAAATAATGCATTTGTTGG
3890 ATAGAAA
1 AT-GAAA
3897 GATACAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.17
21 14 0.58
22 4 0.17
23 2 0.08
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (22 bp):
ATGAAAATAATGCATTTGTTGG
Found at i:7025 original size:6 final size:6
Alignment explanation
Indices: 7009--7046 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
6999 TTCAAAATTG
* *
7009 AAACAA GAACAA AAACAA AAACAA AAAAAA AAACAA AA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AA
7047 TCCAATCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:7692 original size:24 final size:25
Alignment explanation
Indices: 7648--7719 Score: 92
Period size: 24 Copynumber: 2.8 Consensus size: 25
7638 ATAAATTTTT
*
7648 AATTTTTTGATAAATAAAATTTTATTA
1 AATTTTTT-ATAAAT-TAATTTTATTA
*
7675 AATTTTTTATGAA-TAATTTTATTA
1 AATTTTTTATAAATTAATTTTATTA
*
7699 ATTTTTTTATAAATTAATTTT
1 AATTTTTTATAAATTAATTTT
7720 TTTAGAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 21 0.52
25 7 0.17
26 4 0.10
27 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
AATTTTTTATAAATTAATTTTATTA
Found at i:7731 original size:15 final size:16
Alignment explanation
Indices: 7695--7728 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
7685 GAATAATTTT
*
7695 ATTAATTTTTTTATAA
1 ATTAATTTTTTTAGAA
7711 ATTAATTTTTTTAGAA
1 ATTAATTTTTTTAGAA
7727 AT
1 AT
7729 AATGGTGATA
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:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTAATTTTTTTAGAA
Found at i:7863 original size:19 final size:19
Alignment explanation
Indices: 7832--7882 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
7822 TTTAGAAGGA
*
7832 ATTA-ATATGTATTTAATT
1 ATTATATATTTATTTAATT
*
7850 ATTATATATTTATTTTATT
1 ATTATATATTTATTTAATT
*
7869 ATTTTATAATTTAT
1 ATTATAT-ATTTAT
7883 ATTTGAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
20 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTATATATTTATTTAATT
Found at i:8221 original size:3 final size:3
Alignment explanation
Indices: 8213--8275 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
8203 TGAATTTTTA
8213 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8261 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
8276 GTAATACATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9902 original size:25 final size:25
Alignment explanation
Indices: 9868--9918 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
9858 GACTTGTGCC
9868 TTAAGAATATTAGGAAGAAGCAAAG
1 TTAAGAATATTAGGAAGAAGCAAAG
9893 TTAAGAATATTAGGAAGAAGCAAAG
1 TTAAGAATATTAGGAAGAAGCAAAG
9918 T
1 T
9919 GCTGCAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.22
Consensus pattern (25 bp):
TTAAGAATATTAGGAAGAAGCAAAG
Found at i:11917 original size:18 final size:18
Alignment explanation
Indices: 11890--11934 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
11880 TTATCAATCC
* *
11890 CAAATATATCCTCTACCAT
1 CAAATGTATCCCCTACC-T
11909 -AAATGTATCCCCTACCT
1 CAAATGTATCCCCTACCT
11926 CAAATGTAT
1 CAAATGTAT
11935 TATCCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (18 bp):
CAAATGTATCCCCTACCT
Found at i:18032 original size:88 final size:88
Alignment explanation
Indices: 17897--18261 Score: 364
Period size: 88 Copynumber: 4.1 Consensus size: 88
17887 TACTCCAAGA
* * * * **
17897 GGATACTCCAACCCTATTCTAACAAGATTTCAAATTCTTCTTTGTATAATTATATCCTTGGGGAA
1 GGATACTCCAACCCCATTCTAACAAAATTTCAAATT-TTCTTTATATAATTTTATCCTTAAGGAA
*
17962 A-TGCCATCCCTACTATTCTGAAAG
65 ACT-CCATCCCCACTATTCTGAAAG
* * *
17986 GG-CACTCCAACCCCATTCTAACAAAATTTCAAATTTTCTTTCGTATAATTCTATCCTTAAGGAA
1 GGATACTCCAACCCCATTCTAACAAAATTTCAAATTTTCTTT-ATATAATTTTATCCTTAAGGAA
* * **
18050 ACTCCATCGCCACT-TTTTCCAAG
65 ACTCCATCCCCACTATTCTGAAAG
** * * *
18073 GGATACTCCAACCCTGTTTTAACAAAATTTTAAATTTTCTTTCATATAATTTTATTCTTAAGGAA
1 GGATACTCCAACCCCATTCTAACAAAATTTCAAATTTTCTTT-ATATAATTTTATCCTTAAGGAA
* * *
18138 CCTCCATCCCCACTATTTTG-AGG
65 ACTCCATCCCCACTATTCTGAAAG
** * * **
18161 GGATACT-TTACTCCGTTCTAACAAAATTTCAAATTTTCCTTTATATAATTTTATCCTTGGGGAA
1 GGATACTCCAACCCCATTCTAACAAAATTTCAAATTTT-CTTTATATAATTTTATCCTTAAGGAA
* *
18225 ACTTCGATCCCCATTATTCTGAAA-
65 AC-TCCATCCCCACTATTCTGAAAG
18249 GGATACTCCAACC
1 GGATACTCCAACC
18262 TCGTTCTTCA
Statistics
Matches: 228, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
87 58 0.25
88 160 0.70
89 10 0.04
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (88 bp):
GGATACTCCAACCCCATTCTAACAAAATTTCAAATTTTCTTTATATAATTTTATCCTTAAGGAAA
CTCCATCCCCACTATTCTGAAAG
Found at i:22725 original size:32 final size:32
Alignment explanation
Indices: 22684--22756 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
22674 ACAAACCGTA
*
22684 AATGTATCGATACATAAGTGTTGTATTAATAC
1 AATGTATCGATACATAAGTGTTGTATCAATAC
* *
22716 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCAATAC
22748 AATGTATCG
1 AATGTATCG
22757 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCAATAC
Found at i:22799 original size:21 final size:21
Alignment explanation
Indices: 22773--22814 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
22763 AGCTACTGCC
22773 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
22794 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
22815 GTATCGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:22819 original size:13 final size:13
Alignment explanation
Indices: 22801--22828 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22791 ATTAAGGAAA
22801 TGTATCGATACAT
1 TGTATCGATACAT
22814 TGTATCGATACAT
1 TGTATCGATACAT
22827 TG
1 TG
22829 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25250 original size:52 final size:52
Alignment explanation
Indices: 25184--25317 Score: 173
Period size: 52 Copynumber: 2.6 Consensus size: 52
25174 TAAAGTTTCT
* *
25184 CAATTGTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
1 CAATT-TTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
25235 CAATTTTCCTTTAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* *
25288 CAATTTTTCATAATCGAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
25318 TCATTATTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
50 2 0.03
51 6 0.09
52 47 0.67
53 15 0.21
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (52 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:25479 original size:79 final size:79
Alignment explanation
Indices: 25333--25531 Score: 213
Period size: 79 Copynumber: 2.5 Consensus size: 79
25323 ATTTCATCGA
* ** * * ** *
25333 GGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATATTGA
1 GGATACTCCAACCCCATTATTTCCGAAGGGATACTCAAACCCCAACTTTATTCTCAAAATATCGA
* **
25398 TTTCTCATAATTGG
66 TTTCTCACAACCGG
* * **
25412 GGATACTCCAACCCCATTATTTCCGAAGGGATACTCAAATCCCAATTTTATT-TCCTAATCATCG
1 GGATACTCCAACCCCATTATTTCCGAAGGGATACTCAAACCCCAACTTTATTCTCAAAAT-ATCG
25476 ATTTCTCACAACCGG
65 ATTTCTCACAACCGG
* *
25491 GGATACTCCAACCCCATTATTTTC-AAGGGGATACTCCAACC
1 GGATACTCCAACCCCATTATTTCCGAA-GGGATACTCAAACC
25532 TGTTATTATC
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 7 0.07
79 93 0.93
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.29
Consensus pattern (79 bp):
GGATACTCCAACCCCATTATTTCCGAAGGGATACTCAAACCCCAACTTTATTCTCAAAATATCGA
TTTCTCACAACCGG
Found at i:32455 original size:55 final size:55
Alignment explanation
Indices: 32368--32732 Score: 506
Period size: 55 Copynumber: 6.6 Consensus size: 55
32358 AGGAACTCAG
* * * *
32368 AGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCCCTTTCAAAGCCCACAAA
1 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
* *
32423 AGTTGGTGGCA-TTTTCCAGTCCTCAAAAAGCAGCACACCTTTCAAAGCCCACACA
1 AGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
* *
32478 AGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGACACC-TCCTAAAGCCCACACA
1 AGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTTTC-AAAGCCCACACA
* * *
32533 AGTTGGTGGCACCTTTCAGTCCCCAAAGAGTAGGACACCTTTCAAAGCCCACACA
1 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
32588 AGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACA
1 AGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACA
* * * *
32643 AGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCTACACG
1 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
*
32698 AGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
32733 TACACTTTAT
Statistics
Matches: 278, Mismatches: 24, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
54 10 0.04
55 258 0.93
56 10 0.04
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
AGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACA
Found at i:33463 original size:21 final size:21
Alignment explanation
Indices: 33434--33475 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33424 AAAAAAAAAT
*
33434 TTATCCAAATGTATCGATACA
1 TTATACAAATGTATCGATACA
33455 TTATACAAATGTATCGATACA
1 TTATACAAATGTATCGATACA
33476 AGGTCCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
TTATACAAATGTATCGATACA
Found at i:33536 original size:19 final size:19
Alignment explanation
Indices: 33512--33607 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
33502 TTTCAGCGAT
33512 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
33531 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
33545 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
33563 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
* *
33577 -TGTCTCGATACATAAGTG
1 TTGTATCGATACATAAGTA
33595 TTGTATCGATACA
1 TTGTATCGATACA
33608 ATGTATCGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 24
0.67 0.06 0.27
Matches are distributed among these distances:
13 21 0.35
14 1 0.02
16 4 0.07
19 34 0.57
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:33549 original size:32 final size:32
Alignment explanation
Indices: 33513--33620 Score: 189
Period size: 32 Copynumber: 3.4 Consensus size: 32
33503 TTCAGCGATT
*
33513 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
33545 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
33577 TGTCTCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
33609 TGTATCGCTACA
1 TGTATCGATACA
33621 AAGCTACTGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:33550 original size:13 final size:13
Alignment explanation
Indices: 33532--33621 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
33522 ACATAAGTAT
33532 TGTATCGATACAA
1 TGTATCGATACAA
33545 TGTATCGATACATAA
1 TGTATCGATAC--AA
33560 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
33577 TGTCTCGATACATAA
1 TGTATCGATAC--AA
33592 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
33609 TGTATCGCTACAA
1 TGTATCGATACAA
33622 AGCTACTGCC
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 33 0.53
15 4 0.06
17 4 0.06
19 21 0.34
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:36097 original size:50 final size:51
Alignment explanation
Indices: 36038--36134 Score: 139
Period size: 50 Copynumber: 1.9 Consensus size: 51
36028 AATTCTCCGC
36038 AATCGGGGATA-TCCCAACTCCGATTTTATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTTATTTCT-AAAACATC-AATTTTCTAT
36089 AATC-GGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTT
36135 TCATCGAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
50 36 0.84
51 7 0.16
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTCTAT
Found at i:36340 original size:79 final size:80
Alignment explanation
Indices: 36168--36344 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
36158 TTAATCATCT
* * *
36168 GGGATACTCCAACCCCGATATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATT
1 GGGATACTCCAACCCCGATATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATG
*
36233 AATTTCTCATAATCG
66 AATTTCTCACAATCG
* * *
36248 GGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCCCGGTTTTATTTC-CAAATCAT
1 GGGATACTCCAACCCCGATATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAAT-AT
*
36311 CGATTTTC-CACAATCG
65 -GAATTTCTCACAATCG
*
36327 GGGATACTTCAACCCCGA
1 GGGATACTCCAACCCCGA
36345 CTTTATTTTC
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 4 0.05
79 39 0.46
80 42 0.49
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (80 bp):
GGGATACTCCAACCCCGATATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATG
AATTTCTCACAATCG
Found at i:36402 original size:52 final size:51
Alignment explanation
Indices: 36275--36444 Score: 196
Period size: 52 Copynumber: 3.3 Consensus size: 51
36265 TTATCTCCGA
* * * *
36275 GGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* * * **
36326 GGGGATACTTCAACCCCGACTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCC-ACAATC
* * * *
36378 GGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCCACAATC
*
36430 GAGGATACTCCAACC
1 GGGGATACTCCAACC
36445 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
51 38 0.39
52 44 0.45
53 15 0.15
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:36551 original size:290 final size:284
Alignment explanation
Indices: 36037--36624 Score: 792
Period size: 290 Copynumber: 2.1 Consensus size: 284
36027 CAATTCTCCG
* * *
36037 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGATACT
1 CAATCGGGGATACTCCCAACCCCGACTTTATTTTCAAAACACCAATTTTCTATAATCGGGATACT
* *
36101 CCAACTCCGATTTTATTTCTAAAACATCAATTTTTCATCGAGGATACTCCAACCCCGTTAATCAT
66 CCAACTCCGATTTTATTTCAAAAACACCAATTTTTCATCGAGGATACTCCAACCCCGTTAATCAT
** * *
36166 CTGGGATACTCCAACCCCGATATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATA
131 CTGGGATACTCCAACCCCGATATCCTCGAGGGGATACTCCAACCCCCGGCTTTATTCCCAAAATA
**
36231 TTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTT
196 TTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCAATT
36296 TTATTTCCAAATCATCGATTT-TCCA
261 TT-TTTCCAAATCATCGATTTCT-CA
* *
36321 CAATCGGGGATACT-TCAACCCCGACTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
1 CAATCGGGGATACTCCCAACCCCGACTTTATTTTCAAAACACCAATTTT-CTATAATC-GGGATA
* * *
36385 CTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAACCTCGTT
64 CTCCAACTCCGATTTTATTT-CAAAAACACCAATTTTT--C-ATCGAGGATACTCCAACCCCGTT
* * *
36450 ATTTCATC-GAGGATACTCTAACCCCGTTA-CCTCAGAGGGGATACTCCAA-CCCCGGCTTTATT
125 A-ATCATCTG-GGATACTCCAACCCCGATATCCTC-GAGGGGATACTCCAACCCCCGGCTTTATT
* * * *
36512 CCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCA
187 CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCA
* *
36577 ATCCCAATTTTTTTCCTAATCATCGATTTCTCA
252 ACCCCAATTTTTTTCCAAATCATCGATTTCTCA
* *
36610 CAACCGGAGATACTC
1 CAATCGGGGATACTC
36625 TAGCCCTGTT
Statistics
Matches: 265, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
284 42 0.16
285 8 0.03
286 25 0.09
287 15 0.06
289 32 0.12
290 106 0.40
291 37 0.14
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (284 bp):
CAATCGGGGATACTCCCAACCCCGACTTTATTTTCAAAACACCAATTTTCTATAATCGGGATACT
CCAACTCCGATTTTATTTCAAAAACACCAATTTTTCATCGAGGATACTCCAACCCCGTTAATCAT
CTGGGATACTCCAACCCCGATATCCTCGAGGGGATACTCCAACCCCCGGCTTTATTCCCAAAATA
TTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCAATT
TTTTTCCAAATCATCGATTTCTCA
Found at i:41332 original size:28 final size:28
Alignment explanation
Indices: 41244--41502 Score: 329
Period size: 28 Copynumber: 9.0 Consensus size: 28
41234 GCATCAAACA
**
41244 TGAAATGAGTTGCCACCGACTTGTGTAGGCTT
1 TGAAATGA--TGCCACTAACTTGTG--GGCTT
* *
41276 TGAAATGAGTTGTCACTGACTTGTGGGCTT
1 TGAAATGA--TGCCACTAACTTGTGGGCTT
* *
41306 TGAAATGATGCCATTGACTTGTGGGCTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
*
41334 TGAAAAGATGCCACTAACTTGTGGGCTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
* * *
41362 TGAAATGGTGTCGCTAACTTGTGGGCTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
*
41390 TGAAATGATGCCACTAACTTATGGGCTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
*
41418 TGAAATGATGCCACGAACTTGTGGGCTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
*
41446 TGAAAGGATGCCACTAACTTGTGGGCTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
* *
41474 TGAAATGATGCCACGAACTTGTGGACTT
1 TGAAATGATGCCACTAACTTGTGGGCTT
41502 T
1 T
41503 AAAGGGTGCC
Statistics
Matches: 205, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
28 169 0.82
30 13 0.06
32 23 0.11
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (28 bp):
TGAAATGATGCCACTAACTTGTGGGCTT
Found at i:41522 original size:27 final size:27
Alignment explanation
Indices: 41424--42189 Score: 550
Period size: 27 Copynumber: 27.8 Consensus size: 27
41414 GCTTTGAAAT
* * * *
41424 GATGCCACGAACTTGTGGGCTTTGAAAG
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
** * * * *
41452 GATGCCACTAACTTGTGGGCTTTGAAAT
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
* * *
41480 GATGCCACGAACTTGTGGACTTTAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* *
41507 GGTGCCACGGAGTTGTGGACATAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * * *
41534 GGTTCCACAGAGTTGTGGACCTAAAAAG
1 GATGCCACGGAGTTGTGGA-CTTAAAAG
* *
41562 G-TGCCATGGAGTTATGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* *
41588 GGTGCCACGAAGTTGTGGACTTTAAAAG
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
41616 GATGGCATGAAGTTGTGGACCTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * *
41643 GGTGCCATGGAGTTGTGGACATAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * * * *
41670 GGTGCGATGGAGTTGTGGATTTTAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* *
41697 GGTGCCACGGAGTTGTGGGCTTAAAAAG
1 GATGCCACGGAGTTGTGGACTT-AAAAG
* *** * * *
41725 GTGTGCCATTAACTTGTGGGCTTAAAAAA
1 G-ATGCCACGGAGTTGTGGACTT-AAAAG
* * ** *
41754 GATGCCACTGACTTGTAGGTTTTGAAATG
1 GATGCCACGGAGTTGT-GGACTT-AAAAG
* * * **
41783 GGTGCCACTGACTTGT-GAGCTTTGGAAG
1 GATGCCACGGAGTTGTGGA-C-TTAAAAG
* * * *
41811 GGTGCCACTGACTTGTGGGCTTAAAAAG
1 GATGCCACGGAGTTGTGGACTT-AAAAG
* * ** * * **
41839 AGGTACCACTAACTTGTGGGCTTTGGAAG
1 -GATGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
41868 GGTGCCACTGACTTGTAGG-CTTAAAAAA
1 GATGCCACGGAGTTGT-GGACTT-AAAAG
41896 GATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
41923 GATGCCACGGAGTTGTGGATTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* *
41950 GATGGCACAGAGTTGTGGACTTTAAAA-
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
*
41977 GATGCCATGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
42004 GATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
42031 GATGCCACAGAGTTGTGGACTTTAAAAG
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
**
42059 GATGCCATAGAGTTGTGGACTTTAAAAG
1 GATGCCACGGAGTTGTGGAC-TTAAAAG
* * *
42087 GATGCCACTGAGTTATGGACTTAAAAA
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
42114 GATGCCACGAAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
***
42141 GATGCCATTAAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* * *
42168 GATGCCACTGAATCGTGGACTT
1 GATGCCACGGAGTTGTGGACTT
42190 TCAAGAGGTC
Statistics
Matches: 621, Mismatches: 99, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
26 14 0.02
27 330 0.53
28 204 0.33
29 71 0.11
30 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (27 bp):
GATGCCACGGAGTTGTGGACTTAAAAG
Found at i:41760 original size:28 final size:28
Alignment explanation
Indices: 41289--42178 Score: 329
Period size: 28 Copynumber: 32.2 Consensus size: 28
41279 AATGAGTTGT
** * *
41289 CACTGACTTGTGGGCTTTGAAATGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * *
41317 CATTGACTTGTGGGCTTTGAAAA-GATGC
1 CACTGACTTGTGGGC-TTAAAAAGGGTGC
* ** * *
41345 CACTAACTTGTGGGCTTTGAAATGGTGT
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * ** * *
41373 CGCTAACTTGTGGGCTTTGAAATGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * ** * *
41401 CACTAACTTATGGGCTTTGAAATGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
** *
41429 CAC-GAACTTGTGGGCTTTGAAAGGATGC
1 CACTG-ACTTGTGGGCTTAAAAAGGGTGC
* ** * *
41457 CACTAACTTGTGGGCTTTGAAATGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* *
41485 CAC-GAACTTGTGGACTT-TAAAGGGTGC
1 CACTG-ACTTGTGGGCTTAAAAAGGGTGC
* * * * *
41512 CACGGAGTTGTGGACAT-AAAAGGGTTC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * * *
41539 CACAGAGTTGTGGACCTAAAAA-GGTGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * *
41566 CA-TGGAGTTATGGACTT-AAAAGGGTGC
1 CACT-GACTTGTGGGCTTAAAAAGGGTGC
* * * * *
41593 CAC-GAAGTTGTGGACTTTAAAAGGATGG
1 CACTG-ACTTGTGGGCTTAAAAAGGGTGC
* * *
41621 CA-TGAAGTTGTGGACCT-AAAAGGGTGC
1 CACTG-ACTTGTGGGCTTAAAAAGGGTGC
* * *
41648 CA-TGGAGTTGTGGACAT-AAAAGGGTGC
1 CACT-GACTTGTGGGCTTAAAAAGGGTGC
* * * **
41675 GA-TGGAGTTGT-GGATTTTAAAGGGTGC
1 CACT-GACTTGTGGGCTTAAAAAGGGTGC
* *
41702 CACGGAGTTGTGGGCTTAAAAAGGTGTGC
1 CACTGACTTGTGGGCTTAAAAAGG-GTGC
* * * *
41731 CATTAACTTGTGGGCTTAAAAAAGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
** * *
41759 CACTGACTTGTAGGTTTTGAAATGGGTGC
1 CACTGACTTGT-GGGCTTAAAAAGGGTGC
* ***
41788 CACTGACTTGTGAGCTTTGGAAGGGTGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
*
41816 CACTGACTTGTGGGCTTAAAAAGAGGTAC
1 CACTGACTTGTGGGCTTAAAAAG-GGTGC
* ***
41845 CACTAACTTGTGGGCTTTGGAAGGGTGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * *
41873 CACTGACTTGTAGGCTTAAAAAAGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * * *
41901 CACGGAGTTGTGGACTT-AAAAGGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * * * * *
41928 CACGGAGTTGT-GGATTTAAAAGGATGG
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * * * *
41955 CACAGAGTTGTGGACTTTAAAA-GATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * *
41982 CA-TGGAGTTGTGGACTT-AAAAGGATGC
1 CACT-GACTTGTGGGCTTAAAAAGGGTGC
* * * *
42009 CACGGAGTTGTGGACTT-AAAAGGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * * * *
42036 CACAGAGTTGTGGACTTTAAAAGGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * * *
42064 CA-TAGAGTTGTGGACTTTAAAAGGATGC
1 CACT-GACTTGTGGGCTTAAAAAGGGTGC
* * * *
42092 CACTGAGTTATGGACTTAAAAA-GATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
* * *
42119 CAC-GAAGTTGTGGACTT-AAAAGGATGC
1 CACTG-ACTTGTGGGCTTAAAAAGGGTGC
* * * * *
42146 CATTAAGTTGTGGACTT-AAAAGGATGC
1 CACTGACTTGTGGGCTTAAAAAGGGTGC
42173 CACTGA
1 CACTGA
42179 ATCGTGGACT
Statistics
Matches: 719, Mismatches: 112, Indels: 63
0.80 0.13 0.07
Matches are distributed among these distances:
26 19 0.03
27 298 0.41
28 328 0.46
29 74 0.10
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
CACTGACTTGTGGGCTTAAAAAGGGTGC
Found at i:41788 original size:57 final size:58
Alignment explanation
Indices: 41694--41903 Score: 225
Period size: 57 Copynumber: 3.7 Consensus size: 58
41684 GTGGATTTTA
* * * ***
41694 AAGGGTGCCACGGAGTTGT-GGGCTTAAAAAG-GTGTGCCATTAACTTGTGGGCTTAAA
1 AAGGGTGCCACTGACTTGTAGGGCTTAAAAAGAG-GTGCCACTAACTTGTGGGCTTTGG
* * ** * * * *
41751 AAAGATGCCACTGACTTGTAGGTTTTGAAATG-GGTGCCACTGACTTGTGAGCTTTGG
1 AAGGGTGCCACTGACTTGTAGGGCTTAAAAAGAGGTGCCACTAACTTGTGGGCTTTGG
*
41808 AAGGGTGCCACTGACTTGT-GGGCTTAAAAAGAGGTACCACTAACTTGTGGGCTTTGG
1 AAGGGTGCCACTGACTTGTAGGGCTTAAAAAGAGGTGCCACTAACTTGTGGGCTTTGG
*
41865 AAGGGTGCCACTGACTTGTA-GGCTTAAAAA-AGATGCCAC
1 AAGGGTGCCACTGACTTGTAGGGCTTAAAAAGAGGTGCCAC
41904 GGAGTTGTGG
Statistics
Matches: 125, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
56 15 0.12
57 101 0.81
58 9 0.07
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (58 bp):
AAGGGTGCCACTGACTTGTAGGGCTTAAAAAGAGGTGCCACTAACTTGTGGGCTTTGG
Found at i:41825 original size:85 final size:86
Alignment explanation
Indices: 41693--41883 Score: 233
Period size: 86 Copynumber: 2.2 Consensus size: 86
41683 TGTGGATTTT
* * * *** *
41693 AAAGGGTGCCACGGAGTTGTGGGCTTAAAAAGGTGTGCCATTAACTTGTGGGCTTAAAAA-AGAT
1 AAAGGGTGCCACTGACTTGTGAGCTTTGGAAGGTGTGCCACTAACTTGTGGGCTTAAAAAGAGAT
* * *
41757 GCCACTGACTTGTAGGTTTTG
66 ACCACTAACTTGTAGGCTTTG
* *
41778 AAATGGGTGCCACTGACTTGTGAGCTTTGGAAGG-GTGCCACTGACTTGTGGGCTTAAAAAGAGG
1 AAA-GGGTGCCACTGACTTGTGAGCTTTGGAAGGTGTGCCACTAACTTGTGGGCTTAAAAAGAGA
*
41842 TACCACTAACTTGTGGGCTTTG
65 TACCACTAACTTGTAGGCTTTG
*
41864 GAAGGGTGCCACTGACTTGT
1 AAAGGGTGCCACTGACTTGT
41884 AGGCTTAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 44 0.49
86 46 0.51
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (86 bp):
AAAGGGTGCCACTGACTTGTGAGCTTTGGAAGGTGTGCCACTAACTTGTGGGCTTAAAAAGAGAT
ACCACTAACTTGTAGGCTTTG
Found at i:47958 original size:17 final size:17
Alignment explanation
Indices: 47933--47965 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47923 CACATATTTA
*
47933 AAAGGGCACAATAATTC
1 AAAGAGCACAATAATTC
47950 AAAGAGCACAATAATT
1 AAAGAGCACAATAATT
47966 TACTTGTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (17 bp):
AAAGAGCACAATAATTC
Found at i:57375 original size:53 final size:51
Alignment explanation
Indices: 57317--57432 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 51
57307 ACAACGGGGC
*
57317 TAGAGTATCCCCGATTATGGAAAAACAG-TGTTCTAAAAAAATAAAATCGAGGT
1 TAGAGTATCCCCGATTAT-GAAAAACAGATGTT-T-AAAAAATAAAACCGAGGT
*** * *
57370 TAGAGTATCCCCGATTATGAAAATTTGATGTTTTAGAAATAAAACCGAGGT
1 TAGAGTATCCCCGATTATGAAAAACAGATGTTTAAAAAATAAAACCGAGGT
57421 TAGAGTATCCCC
1 TAGAGTATCCCC
57433 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 27 0.48
52 7 0.12
53 22 0.39
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (51 bp):
TAGAGTATCCCCGATTATGAAAAACAGATGTTTAAAAAATAAAACCGAGGT
Found at i:57506 original size:79 final size:79
Alignment explanation
Indices: 57367--57871 Score: 778
Period size: 79 Copynumber: 6.4 Consensus size: 79
57357 ATAAAATCGA
* * * *
57367 GGTTAGAGTATCCCCGATTATGAAAATTTGATGTTTTAGAAATAAAACCGAGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
57432 CTCGAAAATAACGG
66 CTCGAAAATAACGG
* *
57446 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACTGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
57511 CTCGAAAATAACGG
66 CTCGAAAATAACGG
* * *
57525 GGTTGAAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
57590 CTCGGAAATAACGG
66 CTCGAAAATAACGG
* * **
57604 AGTTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
**
57669 CTC-AGAAATAACAA
66 CTCGA-AAATAACGG
* * * *
57683 GGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
57748 CTCAAAAATAACGG
66 CTCGAAAATAACGG
*
57762 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
57827 CTCGAAAATAACGG
66 CTCGAAAATAACGG
* *
57841 GATTGGAGTATCCCCGATTGTGAAAAATTGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGA
57872 CAAACTTAAC
Statistics
Matches: 385, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
79 384 1.00
80 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCGAAAATAACGG
Found at i:59148 original size:35 final size:35
Alignment explanation
Indices: 59083--59269 Score: 331
Period size: 35 Copynumber: 5.4 Consensus size: 35
59073 TCATTTTTAT
*
59083 CCATCATTCCTTGCCTTCA-TTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
59117 CCATCATTCTATGCCTTCATTTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
59152 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
59187 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
59222 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
59257 CCATCATTCCATG
1 CCATCATTCCATG
59270 TTTTTTTATT
Statistics
Matches: 148, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
34 17 0.11
35 131 0.89
ACGTcount: A:0.18, C:0.32, G:0.06, T:0.44
Consensus pattern (35 bp):
CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
Found at i:60138 original size:36 final size:36
Alignment explanation
Indices: 60081--60174 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
60071 ACGCAATACA
* * * *
60081 TCCTACTCTCTAAGGGCAAAAGAAAAATAAAGTTCG
1 TCCTACTCTTTGAGGACAAAAGAAAAATAAAGTGCG
*
60117 -CGCTGCTCTTTGAGGACAAAAGAAAAATAAAGTGCG
1 TC-CTACTCTTTGAGGACAAAAGAAAAATAAAGTGCG
*
60153 TCCTACTCTTTGAGGATAAAAG
1 TCCTACTCTTTGAGGACAAAAG
60175 GGAAAAGAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
35 1 0.02
36 47 0.96
37 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (36 bp):
TCCTACTCTTTGAGGACAAAAGAAAAATAAAGTGCG
Found at i:60292 original size:61 final size:61
Alignment explanation
Indices: 60197--60371 Score: 232
Period size: 61 Copynumber: 2.9 Consensus size: 61
60187 AAAGAAGTGT
* *
60197 GTCCTGCTCTTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGTCTTTGAAAAGA-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAA-GC
* * * *
60258 GTCCTGCTCTATGAGGACTG-GAAGATGCCACCAACTAGTGTGGGATTTGCAAAA-AGAAAGC
1 GTCCTGCTCTTTGAGGACTGAAAAG-TGCCACCAACTTGTGTGGGCTTTG-AAAAGAGAAAGC
*
60319 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG
60372 GCATCCTGCT
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
59 4 0.04
60 3 0.03
61 81 0.83
62 10 0.10
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAAGC
Found at i:60425 original size:94 final size:95
Alignment explanation
Indices: 60320--60492 Score: 280
Period size: 94 Copynumber: 1.8 Consensus size: 95
60310 AAAGAAAGCA
* *
60320 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA-TCCTGCTC
1 TCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AGTCCTACTC
60383 TTTGAGGACT-AAAGGGCGAAAGAAGGGAGCG
64 TTTGAGGACTGAAAGGGCGAAAGAAGGGAGCG
*
60414 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGTCCTACTCTT
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGTCCTACTCTT
60479 TGAGGACTGAAAGG
66 TGAGGACTGAAAGG
60493 TTCCACCAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
93 1 0.01
94 66 0.90
95 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (95 bp):
TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGTCCTACTCTT
TGAGGACTGAAAGGGCGAAAGAAGGGAGCG
Found at i:60538 original size:155 final size:152
Alignment explanation
Indices: 60256--60553 Score: 406
Period size: 155 Copynumber: 1.9 Consensus size: 152
60246 AAAAGAAAAG
60256 GCGTCCTGCTCTATGAGGACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCAT
1 GCGTCCTGCTCTATGAGGACTGGAAGATGCCACCAACTAGTGTGGGATTT-CAAAAAG-AAG-AT
* *
60321 CCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTT
63 CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCTTT
60386 GAGGACTAAAGGGCGAAAGAAGGGA
128 GAGGACTAAAGGGCGAAAGAAGGGA
* * *
60411 GCGTCCTGCTCTTTGAGGACTAGGAAG-TGCCACCAACTTGTGTGGGCTTT-AAAAAG-AG-TCC
1 GCGTCCTGCTCTATGAGGACT-GGAAGATGCCACCAACTAGTGTGGGATTTCAAAAAGAAGATCC
* * *
60472 TACTCTTTGAGGACTGAAAGGTTCCACCAACTTGTATGGGCTTTGAAAGGCGAAGGCGTCCTGCT
65 TACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGCTTT--AA----AAGGCATCCTGCT
60537 CTTTGAGGACTAAAGGG
124 CTTTGAGGACTAAAGGG
60554 TGCCACCAAC
Statistics
Matches: 128, Mismatches: 8, Indels: 14
0.85 0.05 0.09
Matches are distributed among these distances:
149 43 0.34
151 4 0.03
153 6 0.05
155 70 0.55
156 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (152 bp):
GCGTCCTGCTCTATGAGGACTGGAAGATGCCACCAACTAGTGTGGGATTTCAAAAAGAAGATCCT
ACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCTTTGAG
GACTAAAGGGCGAAAGAAGGGA
Found at i:60563 original size:61 final size:61
Alignment explanation
Indices: 60411--61026 Score: 879
Period size: 61 Copynumber: 10.3 Consensus size: 61
60401 AAAGAAGGGA
60411 GCGTCCTGCTCTTTGAGGACT--AGGAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAA-
1 GCGTCCTGCTCTTTGAGGACTAAAGG--GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * * * * **
60466 GAGTCCTACTCTTTGAGGACTGAAA-GGTTCCACCAACTTGTATGGGCTTTGAAAGGCGAAG
1 GCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
60527 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
60588 ACATCCTGCTCTTTAAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
60649 GCATCCTGATCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
60710 GCGTCCTGCTCTTTGAGGACTAGAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
60771 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* **
60832 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
60893 GCATCCTGCTCTTTGAGGA-TAAAGGGTGCCACCAACTTGTGTGGACTTT-AAAGG---A-
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
60948 --GTCCTGCTCTTTGAGGACTGAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
61008 GCATCCTGCTCTTTGAGGA
1 GCGTCCTGCTCTTTGAGGA
61027 TTGAAATGGC
Statistics
Matches: 507, Mismatches: 35, Indels: 31
0.88 0.06 0.05
Matches are distributed among these distances:
53 16 0.03
54 1 0.00
55 69 0.14
56 6 0.01
57 1 0.00
58 2 0.00
59 6 0.01
60 34 0.07
61 356 0.70
62 16 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
Found at i:60565 original size:210 final size:215
Alignment explanation
Indices: 60197--60614 Score: 528
Period size: 210 Copynumber: 1.9 Consensus size: 215
60187 AAAGAAGTGT
* * *
60197 GTCCTGCTCTTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGTCTTTGAAAAGAAAAGGCGTCC
1 GTCCTGCTCTTTGAGGATAGAAAAGTGCCACCAACTTGTGTGGGCTTT---AAGAAAAGGAGTCC
* * *
60262 TGCTCTATGAGGACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCATCCTGCT
63 TACTCTATGAGGACTGAAAGATGCCACCAACTAGTATGGGATTTGCAAAAAGAAAGCATCCTGCT
*
60327 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-G-CATCCTGCTCTTTGAGG
128 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGACATCCTGCTCTTTAAGG
60390 ACTAAAGGGCGAAAGAAGGGAGC
193 ACTAAAGGGCGAAAGAAGGGAGC
*
60413 GTCCTGCTCTTTGAGGACTAG-GAAGTGCCACCAACTTGTGTGGGCTTT-A-AAAA-GAGTCCTA
1 GTCCTGCTCTTTGAGGA-TAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAAGGAGTCCTA
* * * * * ** * *
60474 CTCTTTGAGGACTGAAAGGTTCCACCAACTTGTATGGGCTTTG-AAAGGCGAAGGCGTCCTGCTC
65 CTCTATGAGGACTGAAAGATGCCACCAACTAGTATGGGATTTGCAAA-AAGAAAGCATCCTGCTC
*
60538 TTTGAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGACATCCTGCTCTTT
129 TTTGAGGACTGAAA-AGTGCCACCAACTTGTGTGGGCTTTAAAAG----AGACATCCTGCTCTTT
60602 AAGGACTAAAGGG
189 AAGGACTAAAGGG
60615 TGCCACCAAC
Statistics
Matches: 175, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
209 6 0.03
210 94 0.54
211 4 0.02
212 1 0.01
215 1 0.01
216 67 0.38
217 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (215 bp):
GTCCTGCTCTTTGAGGATAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAAGGAGTCCTAC
TCTATGAGGACTGAAAGATGCCACCAACTAGTATGGGATTTGCAAAAAGAAAGCATCCTGCTCTT
TGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGACATCCTGCTCTTTAAGGACT
AAAGGGCGAAAGAAGGGAGC
Found at i:60945 original size:29 final size:29
Alignment explanation
Indices: 60912--60999 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
60902 TCTTTGAGGA
60912 TAAAGGGTGCCACCAACTTGTGTGGACTT
1 TAAAGGGTGCCACCAACTTGTGTGGACTT
** * *
60941 TAAAGGAGT-CCTGC-TCTT-TGAGGAC-T
1 TAAAGG-GTGCCACCAACTTGTGTGGACTT
* *
60967 GAAAGGGTGCCACCAACTTGTGTGGGCTT
1 TAAAGGGTGCCACCAACTTGTGTGGACTT
60996 TAAA
1 TAAA
61000 AGGAAAAGGC
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
25 2 0.05
26 9 0.21
27 9 0.21
28 8 0.19
29 13 0.30
30 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (29 bp):
TAAAGGGTGCCACCAACTTGTGTGGACTT
Found at i:67177 original size:53 final size:51
Alignment explanation
Indices: 67119--67234 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 51
67109 ACAACGGGGC
*
67119 TAGAGTATCCCCGATTATGGAAAAA-CGATGTTCTAAAAAAATAAAATCGAGGT
1 TAGAGTATCCCCGATTAT-GAAAAATCGATGTT-T-AAAAAATAAAACCGAGGT
* * * *
67172 TAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGT
1 TAGAGTATCCCCGATTATGAAAAATCGATGTTTAAAAAATAAAACCGAGGT
*
67223 TGGAGTATCCCC
1 TAGAGTATCCCC
67235 TCAGAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 25 0.45
52 7 0.12
53 24 0.43
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (51 bp):
TAGAGTATCCCCGATTATGAAAAATCGATGTTTAAAAAATAAAACCGAGGT
Found at i:67233 original size:51 final size:51
Alignment explanation
Indices: 67087--67234 Score: 156
Period size: 53 Copynumber: 2.8 Consensus size: 51
67077 TGACGAGAAA
* * * *
67087 AAAAATTGGTATTTTAGAGATAACAACGGGGCTAGAGTATCCCCGATTATGG
1 AAAAATTGATGTTTTAGAAATAA-AACGGGGTTAGAGTATCCCCGATTATGG
* * * *
67139 AAAAA-CGATGTTCTAAAAAAATAAAATCGAGGTTAGAGTATCCCCGATTAT-G
1 AAAAATTGATGTT-T-TAGAAATAAAA-CGGGGTTAGAGTATCCCCGATTATGG
*
67191 AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 AAAAATTGATGTTTTAGAAATAAAA-CGGGGTTAGAGTATCCCC
67235 TCAGAAATAA
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
51 29 0.37
52 15 0.19
53 34 0.44
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (51 bp):
AAAAATTGATGTTTTAGAAATAAAACGGGGTTAGAGTATCCCCGATTATGG
Found at i:67308 original size:79 final size:79
Alignment explanation
Indices: 67169--67672 Score: 866
Period size: 79 Copynumber: 6.4 Consensus size: 79
67159 ATAAAATCGA
*
67169 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
67234 CTCAGAAATAACGG
66 CTCGGAAATAACGG
* * *
67248 GGTTGGAGTATCCACGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
67313 CTCGGAAATAACGG
66 CTCGGAAATAACGG
* * *
67327 GGTTGGAGAATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
67392 CTCGGAAATAACGG
66 CTCGGAAATAACGG
*
67406 GGTTGGAGTATCCCCGATTATG-AAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
67470 CTCTGAAATAACGG
66 CTCGGAAATAACGG
* *
67484 GGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
67549 CTCGAAAATAACGG
66 CTCGGAAATAACGG
67563 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
67628 CTCGGAAATAACGG
66 CTCGGAAATAACGG
* *
67642 GATTGGAGTATCCCCGATTGTGAAAAATTGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGA
67673 GAAACTTAAC
Statistics
Matches: 398, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
78 74 0.19
79 324 0.81
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCGGAAATAACGG
Found at i:67485 original size:236 final size:237
Alignment explanation
Indices: 67169--67672 Score: 875
Period size: 236 Copynumber: 2.1 Consensus size: 237
67159 ATAAAATCGA
*
67169 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
* * *
67234 CTCAGAAATAACGGGGTTGGAGTATCCACGATTATGAAAAATTGATGTTTTAGAGATAAAACCGG
66 CTCAGAAATAACGGGGTTGGAGTATCCACGATTATGAAAAATTAATATTTTAGAAATAAAACCGG
* *
67299 GGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGAATCCCCGATTATGAAAAATTGGTGTTTT
131 GGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGAATCCCCGATTATGAAAAATTGATGTTTT
*
67364 AGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGG
196 AGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGG
*
67406 GGTTGGAGTATCCCCGATTATG-AAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
* *
67470 CTCTGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCGG
66 CTCAGAAATAACGGGGTTGGAGTATCCACGATTATGAAAAATTAATATTTTAGAAATAAAACCGG
* *
67535 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTT
131 GGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGAATCCCCGATTATGAAAAATTGATGTTTT
67600 AGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGG
196 AGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGG
* *
67642 GATTGGAGTATCCCCGATTGTGAAAAATTGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGA
67673 GAAACTTAAC
Statistics
Matches: 252, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
236 223 0.88
237 29 0.12
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (237 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCAGAAATAACGGGGTTGGAGTATCCACGATTATGAAAAATTAATATTTTAGAAATAAAACCGG
GGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGAATCCCCGATTATGAAAAATTGATGTTTT
AGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGG
Found at i:68949 original size:35 final size:35
Alignment explanation
Indices: 68884--69140 Score: 453
Period size: 35 Copynumber: 7.4 Consensus size: 35
68874 TCATTTTTAT
68884 CCATCATTCCATGCCTTCATTTTT-TATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
* * *
68918 CCATCATTCTATGGCTTCATTTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
*
68953 CCATCATTCCATGCTTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
* *
68988 CCATCATTCTATGCCTTCATTTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
69023 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
69058 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
69093 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
69128 CCATCATTCCATG
1 CCATCATTCCATG
69141 TTTTTTTATT
Statistics
Matches: 211, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
34 22 0.10
35 189 0.90
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.44
Consensus pattern (35 bp):
CCATCATTCCATGCCTTCATTTTTATATTCCATGC
Found at i:71270 original size:29 final size:30
Alignment explanation
Indices: 71237--71298 Score: 117
Period size: 29 Copynumber: 2.1 Consensus size: 30
71227 ATTTACCCAC
71237 TTACTTTTAAAAATACTAGCCATTTA-TTT
1 TTACTTTTAAAAATACTAGCCATTTACTTT
71266 TTACTTTTAAAAATACTAGCCATTTACTTT
1 TTACTTTTAAAAATACTAGCCATTTACTTT
71296 TTA
1 TTA
71299 AAACTACCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (30 bp):
TTACTTTTAAAAATACTAGCCATTTACTTT
Found at i:73300 original size:22 final size:21
Alignment explanation
Indices: 73273--73323 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
73263 AATATCATGT
73273 TTATATTATT-TTATGTATTATA
1 TTATATT-TTATTAT-TATTATA
*
73295 TTATATTTTAATTATTTTTATA
1 TTATATTTT-ATTATTATTATA
73317 TTATATT
1 TTATATT
73324 CATATCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 20 0.77
23 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATATTTTATTATTATTATA
Found at i:73319 original size:11 final size:12
Alignment explanation
Indices: 73290--73323 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
73280 ATTTTATGTA
73290 TTATATTATATT
1 TTATATTATATT
73302 TTA-ATTAT-TT
1 TTATATTATATT
73312 TTATATTATATT
1 TTATATTATATT
73324 CATATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.25
11 10 0.50
12 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATTATATT
Found at i:76562 original size:13 final size:13
Alignment explanation
Indices: 76546--76571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76536 TAGAGTAGCT
76546 TTGTATCGATACA
1 TTGTATCGATACA
76559 TTGTATCGATACA
1 TTGTATCGATACA
76572 ACACTTATGT
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):
TTGTATCGATACA
Found at i:77639 original size:19 final size:20
Alignment explanation
Indices: 77615--77662 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
77605 CTCATTATAT
77615 TATTAAAA-TATA-ATTTTTA
1 TATTAAAATTATATA-TTTTA
77634 TATTAATAATTATATATTTTA
1 TATTAA-AATTATATATTTTA
77655 TAATTAAA
1 T-ATTAAA
77663 TTTAAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 11 0.44
22 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAAATTATATATTTTA
Found at i:79269 original size:21 final size:21
Alignment explanation
Indices: 79250--79293 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
79240 TTGTTTATTT
79250 TATTAAATATATTTTATATTAA
1 TATT-AATATATTTTATATTAA
*
79272 TATTTATATATTTTATAATTAA
1 TATTAATATATTTTAT-ATTAA
79294 ATTTAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATATATTTTATATTAA
Found at i:79297 original size:21 final size:21
Alignment explanation
Indices: 79256--79298 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
79246 ATTTTATTAA
79256 ATATATTTTATATTAATATTT
1 ATATATTTTATATTAATATTT
79277 ATATATTTTATAATTAA-ATTT
1 ATATATTTTAT-ATTAATATTT
79298 A
1 A
79299 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTTTATATTAATATTT
Found at i:79321 original size:19 final size:19
Alignment explanation
Indices: 79293--79335 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
79283 TTTATAATTA
79293 AATTTAAATA-AAAATATAT
1 AATTTAAATATAAAA-ATAT
*
79312 AATTTTAATATAAAAATAT
1 AATTTAAATATAAAAATAT
*
79331 TATTT
1 AATTT
79336 CAAGTCGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTAAATATAAAAATAT
Found at i:80006 original size:17 final size:17
Alignment explanation
Indices: 79955--80007 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
79945 TAATGTCTCC
79955 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
79970 AAA-TTAT-TAAGATATCA
1 AAATTTATATAA-ATAT-A
79987 AAATTTATATAAATATA
1 AAATTTATATAAATATA
80004 AAAT
1 AAAT
80008 ATATTAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 7 0.22
17 8 0.25
18 8 0.25
19 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:84126 original size:19 final size:20
Alignment explanation
Indices: 84081--84130 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
84071 ACACCCAGAT
*
84081 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGCATA
* *
84101 ATATCGATACATGTT-CATA
1 GTATCGATACATATTGCATA
84120 GTATCGATACA
1 GTATCGATACA
84131 CCTTAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (20 bp):
GTATCGATACATATTGCATA
Found at i:87820 original size:51 final size:51
Alignment explanation
Indices: 87743--87882 Score: 235
Period size: 51 Copynumber: 2.7 Consensus size: 51
87733 TTCATGCAAC
* * *
87743 TAATACCAAAAGTTTATGCAAGCTCTCCCCCTTAATACAAATGTTCTTCCCTT
1 TAATA-CAAAA-TTTATACAAACTCTCCCCCTTAATACAAATGTTATTCCCTT
87796 TAATACAAAATTTATACAAACTCTCCCCCTTAATACAAATGTTATTCCCTT
1 TAATACAAAATTTATACAAACTCTCCCCCTTAATACAAATGTTATTCCCTT
87847 TAATACAAAATTTATACAAACTCTCCCCCTTAATAC
1 TAATACAAAATTTATACAAACTCTCCCCCTTAATAC
87883 GTTATCACCC
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
51 74 0.88
52 5 0.06
53 5 0.06
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (51 bp):
TAATACAAAATTTATACAAACTCTCCCCCTTAATACAAATGTTATTCCCTT
Found at i:87831 original size:30 final size:30
Alignment explanation
Indices: 87795--87882 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
87785 GTTCTTCCCT
87795 TTAATACAAAATTTATACAAACTCTCCCCC
1 TTAATACAAAATTTATACAAACTCTCCCCC
* *
87825 TTAATAC-AAATGT-T----A-T-T-CCCT
1 TTAATACAAAATTTATACAAACTCTCCCCC
87846 TTAATACAAAATTTATACAAACTCTCCCCC
1 TTAATACAAAATTTATACAAACTCTCCCCC
87876 TTAATAC
1 TTAATAC
87883 GTTATCACCC
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
21 10 0.22
22 6 0.13
23 2 0.04
24 1 0.02
27 1 0.02
28 2 0.04
29 6 0.13
30 17 0.38
ACGTcount: A:0.39, C:0.26, G:0.01, T:0.34
Consensus pattern (30 bp):
TTAATACAAAATTTATACAAACTCTCCCCC
Found at i:90494 original size:21 final size:21
Alignment explanation
Indices: 90468--90527 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
90458 TTTTTATTAG
90468 CTAACTCA-TCATTTTCATTTT
1 CTAACTCATTCATTTTC-TTTT
90489 GC-AACTCATTTC-TTTTCTTTT
1 -CTAACTCA-TTCATTTTCTTTT
90510 CTAACTCATTCATTTTCT
1 CTAACTCATTCATTTTCT
90528 CCTCTAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.12
21 22 0.65
22 6 0.18
23 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.53
Consensus pattern (21 bp):
CTAACTCATTCATTTTCTTTT
Found at i:90533 original size:21 final size:21
Alignment explanation
Indices: 90491--90534 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
90481 TTCATTTTGC
**
90491 AACTCATTTCTTTTCTTTTCT
1 AACTCATTTCTTTTCTCCTCT
90512 AACTCA-TTCATTTTCTCCTCT
1 AACTCATTTC-TTTTCTCCTCT
90533 AA
1 AA
90535 TTCACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.52
Consensus pattern (21 bp):
AACTCATTTCTTTTCTCCTCT
Found at i:94923 original size:38 final size:38
Alignment explanation
Indices: 94881--94982 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
94871 TATTAAACTG
* * *
94881 TGTCACTAGTTAAGAATAGTGGTTTTCGTTTCTAACCA
1 TGTCACTAGTTTAGAATAGTGGTTTTCATTTATAACCA
* *
94919 TGTCACT-GATTTAGAATAGTGATTTTCATTTATAACTA
1 TGTCACTAG-TTTAGAATAGTGGTTTTCATTTATAACCA
* *
94957 TGTCATTAGTTTAGAATAGTAGTTTT
1 TGTCACTAGTTTAGAATAGTGGTTTT
94983 TATCTATAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
37 1 0.02
38 52 0.96
39 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (38 bp):
TGTCACTAGTTTAGAATAGTGGTTTTCATTTATAACCA
Found at i:95857 original size:20 final size:21
Alignment explanation
Indices: 95832--95876 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
95822 GTTTAGATGA
95832 AAAACAA-GCATTGGTTGGAT
1 AAAACAATGCATTGGTTGGAT
*
95852 AAAACAATGCATTTGTTGGAT
1 AAAACAATGCATTGGTTGGAT
95873 AAAA
1 AAAA
95877 AGATACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (21 bp):
AAAACAATGCATTGGTTGGAT
Found at i:96624 original size:23 final size:23
Alignment explanation
Indices: 96560--96616 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
96550 ATAACATTTA
* *
96560 AAAATAATTAATTACATTAAAACT
1 AAAATAATAAAAT-CATTAAAACT
*
96584 ATAATAATAAAATCATTAAAAC-
1 AAAATAATAAAATCATTAAAACT
96606 AAAATAATAAA
1 AAAATAATAAA
96617 CCTTATTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 9 0.31
24 10 0.34
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATAATAAAATCATTAAAACT
Found at i:98058 original size:18 final size:19
Alignment explanation
Indices: 98014--98060 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
98004 TCTTTTTTTT
* *
98014 TTACAAATTTTTTTGGTGTC
1 TTAC-AATTTTTTTGGAGTA
*
98034 TTTCAATTTTTTTGGAG-A
1 TTACAATTTTTTTGGAGTA
98052 TTACAATTT
1 TTACAATTT
98061 CTCCATGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (19 bp):
TTACAATTTTTTTGGAGTA
Found at i:104890 original size:9 final size:9
Alignment explanation
Indices: 104876--104920 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
104866 AAGGTTCAAC
104876 AAAAAAAAG
1 AAAAAAAAG
104885 AAAAAAAAG
1 AAAAAAAAG
*
104894 AAGAAAAAG
1 AAAAAAAAG
104903 -AAAAAAAG
1 AAAAAAAAG
*
104911 AAAGAAAAG
1 AAAAAAAAG
104920 A
1 A
104921 GAGAAGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:106757 original size:97 final size:97
Alignment explanation
Indices: 106623--106818 Score: 338
Period size: 97 Copynumber: 2.0 Consensus size: 97
106613 AAAATTCTTT
* * * * *
106623 TTATCGAGGATACTCTAACCCTATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCA
1 TTATCGAGGACACTCCAACCCCATTCCTCCAAAGGGATACTCCAACCCCGCTTTTAAACACATCA
*
106688 AAGTTTAAATCTTATTCTCACTTAAATTGTCA
66 AAGTTTAAATCTTATTCTCACTCAAATTGTCA
106720 TTATCGAGGACACTCCAACCCCATTCCTCCAAAGGGATACTCCAACCCCGCTTTTAAACACATCA
1 TTATCGAGGACACTCCAACCCCATTCCTCCAAAGGGATACTCCAACCCCGCTTTTAAACACATCA
106785 AAGTTTAAATCTTATTCTCACTCAAATTGTCA
66 AAGTTTAAATCTTATTCTCACTCAAATTGTCA
106817 TT
1 TT
106819 CTCACTCAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 93 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (97 bp):
TTATCGAGGACACTCCAACCCCATTCCTCCAAAGGGATACTCCAACCCCGCTTTTAAACACATCA
AAGTTTAAATCTTATTCTCACTCAAATTGTCA
Found at i:106821 original size:18 final size:18
Alignment explanation
Indices: 106798--106835 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
106788 TTTAAATCTT
106798 ATTCTCACTCAAATTGTC
1 ATTCTCACTCAAATTGTC
106816 ATTCTCACTCAAATTGTC
1 ATTCTCACTCAAATTGTC
106834 AT
1 AT
106836 CATCGGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.39
Consensus pattern (18 bp):
ATTCTCACTCAAATTGTC
Found at i:108752 original size:3 final size:3
Alignment explanation
Indices: 108744--108774 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
108734 TATATCCACC
108744 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
108775 ATTTTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:111810 original size:22 final size:22
Alignment explanation
Indices: 111780--111855 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
111770 ATTACTGTTG
111780 ATCACTGTTCATGTATCAATAC
1 ATCACTGTTCATGTATCAATAC
* * * *
111802 ATCATTGTTCA--TAACTATTC
1 ATCACTGTTCATGTATCAATAC
*
111822 ATCACTATTCATGTATCAATAC
1 ATCACTGTTCATGTATCAATAC
*
111844 ATCATTGTTCAT
1 ATCACTGTTCAT
111856 CACTGTTTAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 15 0.37
22 26 0.63
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (22 bp):
ATCACTGTTCATGTATCAATAC
Found at i:113123 original size:15 final size:15
Alignment explanation
Indices: 113103--113134 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
113093 CAAGCTTGCT
113103 ACCACACATGAGGGG
1 ACCACACATGAGGGG
113118 ACCACACATGAGGGG
1 ACCACACATGAGGGG
113133 AC
1 AC
113135 AAACCAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.28, G:0.31, T:0.06
Consensus pattern (15 bp):
ACCACACATGAGGGG
Found at i:117609 original size:13 final size:13
Alignment explanation
Indices: 117591--117628 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
117581 ACATAAGTGT
117591 TGTATCGATACAA
1 TGTATCGATACAA
*
117604 TGTATCGATATAA
1 TGTATCGATACAA
117617 TGTATCGATACA
1 TGTATCGATACA
117629 TAAGTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:121437 original size:19 final size:19
Alignment explanation
Indices: 121413--121463 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
121403 TTTCAATGAT
121413 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
121432 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
121451 TTGTATCGATACA
1 TTGTATCGATACA
121464 ATGTATCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:121593 original size:52 final size:52
Alignment explanation
Indices: 121549--121677 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
121539 CACTGATCTT
121549 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
121601 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
121653 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
121678 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:122548 original size:20 final size:20
Alignment explanation
Indices: 122523--122571 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
122513 AAACCTTGAG
122523 CATGCATTTTTACTATGTTT
1 CATGCATTTTTACTATGTTT
122543 CATGCATTTTTACTATGTTT
1 CATGCATTTTTACTATGTTT
*
122563 CATACATTT
1 CATGCATTT
122572 ATGGCATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.53
Consensus pattern (20 bp):
CATGCATTTTTACTATGTTT
Found at i:129607 original size:30 final size:29
Alignment explanation
Indices: 129519--129786 Score: 176
Period size: 30 Copynumber: 8.6 Consensus size: 29
129509 AAAATCCATG
* *
129519 ACTCAGTGGCATCTTTTCTTCAAAGTCCACG
1 ACTCAGTGGCATC-TTT-TTCTAAGTCCACA
* * * *
129550 ACCCAAGTGGCAATATCTTTTCAAAGTCCATA
1 ACTC-AGTGGC-ATCT-TTTTCTAAGTCCACA
* *
129582 ACTTAGTGGCATCCTTTTTCTAAGTCCACG
1 ACTCAGTGGCAT-CTTTTTCTAAGTCCACA
129612 ACTCAGTGGCATCCTTTTCTTCCTAAAGTCCACA
1 ACTCAGTGGCAT-C-TTT-TT-CT-AAGTCCACA
* * *
129646 ACTCAGTGGCAATCTCTTCTCAAAGTCCACG
1 ACTCAGTGGC-ATCT-TTTTCTAAGTCCACA
*
129677 ACTCAGTGGCATCTTTTTCCTAAAGTCCACG
1 ACTCAGTGGCATCTTTTT-CT-AAGTCCACA
* * * *
129708 ACTCAAGTGCCATCTCTTGTCCAAGTCCACG
1 ACTC-AGTGGCATCT-TTTTCTAAGTCCACA
* ** * *
129739 ATTCAGTGGCATCTTGTACCAAAATCCACA
1 ACTCAGTGGCATCTT-TTTCTAAGTCCACA
*
129769 ACTCCGTGGCATCTTTTT
1 ACTCAGTGGCATCTTTTT
129787 TCCTTTTAAG
Statistics
Matches: 191, Mismatches: 31, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
29 5 0.03
30 63 0.33
31 56 0.29
32 33 0.17
33 11 0.06
34 21 0.11
35 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (29 bp):
ACTCAGTGGCATCTTTTTCTAAGTCCACA
Found at i:129671 original size:31 final size:30
Alignment explanation
Indices: 129503--129782 Score: 217
Period size: 31 Copynumber: 9.0 Consensus size: 30
129493 TCAAATCTCA
* *
129503 CTTCTCAAAATCCATGACTCAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
* * *
129533 TTTCTTCAAAGTCCACGACCCAAGTGGCAATAT
1 CTTC-TCAAAGTCCACGACTC-AGTGGC-ATCT
* ** *
129566 CTTTTCAAAGTCCATAACTTAGTGGCATC-
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
* *
129595 CTTTTTCTAAGTCCACGACTCAGTGGCATCCT
1 C-TTCTCAAAGTCCACGACTCAGTGGCAT-CT
* *
129627 TTTCTTCCTAAAGTCCACAACTCAGTGGCAATCT
1 CTTC-T-C-AAAGTCCACGACTCAGTGGC-ATCT
129661 CTTCTCAAAGTCCACGACTCAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
* *
129691 -TTTTCCTAAAGTCCACGACTCAAGTGCCATCT
1 CTTCT-C-AAAGTCCACGACTC-AGTGGCATCT
* * *
129723 CTTGTCCAAGTCCACGATTCAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCAGTGGCATCT
* * *
129753 -TGTAC-CAAAATCCACAACTCCGTGGCATCT
1 CT-T-CTCAAAGTCCACGACTCAGTGGCATCT
129783 TTTTTCCTTT
Statistics
Matches: 200, Mismatches: 34, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
29 5 0.03
30 63 0.31
31 67 0.34
32 30 0.15
33 10 0.05
34 23 0.12
35 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (30 bp):
CTTCTCAAAGTCCACGACTCAGTGGCATCT
Found at i:129685 original size:95 final size:95
Alignment explanation
Indices: 129513--129721 Score: 273
Period size: 95 Copynumber: 2.2 Consensus size: 95
129503 CTTCTCAAAA
* * *
129513 TCCATGACTCAGTGGCAT-CTTTTCTTCAAAGTCCACGACCCAAGTGGCAATATCTTTTCAAAGT
1 TCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACAACCCAAGTGGCAATATCTTCTCAAAGT
* *
129577 CCATAACTTAGTGGCATCCTTTTT-CT-AAG
66 CCACAACTCAGTGGCAT-CTTTTTCCTAAAG
* *
129606 TCCACGACTCAGTGGCATCCTTTTCTTCCTAAAGTCCACAACTC-AGTGGCAATCTCTTCTCAAA
1 TCCACGACTCAGTGGCATCCTTTTCTT-C-AAAGTCCACAACCCAAGTGGCAATATCTTCTCAAA
*
129670 GTCCACGACTCAGTGGCATCTTTTTCCTAAAG
64 GTCCACAACTCAGTGGCATCTTTTTCCTAAAG
*
129702 TCCACGACTCAAGTGCCATC
1 TCCACGACTC-AGTGGCATC
129722 TCTTGTCCAA
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
93 17 0.17
94 14 0.14
95 37 0.37
96 25 0.25
97 8 0.08
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.31
Consensus pattern (95 bp):
TCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACAACCCAAGTGGCAATATCTTCTCAAAGT
CCACAACTCAGTGGCATCTTTTTCCTAAAG
Found at i:129745 original size:127 final size:127
Alignment explanation
Indices: 129519--129751 Score: 296
Period size: 127 Copynumber: 1.8 Consensus size: 127
129509 AAAATCCATG
* *
129519 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACCCAAGTGGCAATATCTTTTCAAAGTCCATAAC
1 ACTCAGTGGCATCTCTTCTTCAAAGTCCACGACCCAAGTGGCAATATCTTTTCAAAGTCCACAAC
* * * *
129584 TTAGTGGCATCCTTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCTAAAGTCCACA
66 TAAGTGCCATCCTTTGTCCAAGTCCACGACTCAGTGGCATCCTTTTCTTCCTAAAGTCCACA
* *
129646 ACTCAGTGGCAATCTCTTC-TCAAAGTCCACGACTC-AGTGGC-ATCT-TTTTCCTAAAGTCCAC
1 ACTCAGTGGC-ATCTCTTCTTCAAAGTCCACGACCCAAGTGGCAATATCTTTT-C-AAAGTCCAC
* *
129707 GACTCAAGTGCCAT-CTCTTGTCCAAGTCCACGATTCAGTGGCATC
63 AACT-AAGTGCCATCCT-TTGTCCAAGTCCACGACTCAGTGGCATC
129752 TTGTACCAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
124 4 0.04
125 4 0.04
126 19 0.21
127 57 0.63
128 7 0.08
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (127 bp):
ACTCAGTGGCATCTCTTCTTCAAAGTCCACGACCCAAGTGGCAATATCTTTTCAAAGTCCACAAC
TAAGTGCCATCCTTTGTCCAAGTCCACGACTCAGTGGCATCCTTTTCTTCCTAAAGTCCACA
Found at i:129814 original size:158 final size:158
Alignment explanation
Indices: 129503--129790 Score: 363
Period size: 157 Copynumber: 1.8 Consensus size: 158
129493 TCAAATCTCA
* *
129503 CTTCTCAAAATCCATGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACCCAAGTGGCAATATCT
1 CTTCTCAAAATCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACGACCCAAGTGGCAATATCT
* * ** * * *
129568 TTTCAAAGTCCATAACTTAGTGGCATCCTTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTT
66 TGTCAAAGTCCACAACTTAGTGGCATCCTTTACCAAAATCCACAACTCAGTGGCATCCTTTTCTT
129633 CCTAAAGTCCACAACTCAGTGGCAATCT
131 CCTAAAGTCCACAACTCAGTGGCAATCT
* * * *
129661 CTTCTCAAAGTCCACGACTCAGTGGCATCTTTTTCCT-AAAGTCCACGACTCAAGT-GCCATCTC
1 CTTCTCAAAATCCACGACTCAGTGGCATC-TTTTCCTCAAAGTCCACGACCCAAGTGGCAATATC
* * *
129724 TTGTCCAAGTCCACGA-TTCAGTGGCAT-CTTGTACCAAAATCCACAACTCCGTGGCAT-CTTTT
65 TTGTCAAAGTCCACAACTT-AGTGGCATCCTT-TACCAAAATCCACAACTCAGTGGCATCCTTTT
129786 -TTCCT
128 CTTCCT
129791 TTTAAGTCCT
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
155 5 0.05
156 10 0.09
157 46 0.41
158 44 0.40
159 6 0.05
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (158 bp):
CTTCTCAAAATCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACGACCCAAGTGGCAATATCT
TGTCAAAGTCCACAACTTAGTGGCATCCTTTACCAAAATCCACAACTCAGTGGCATCCTTTTCTT
CCTAAAGTCCACAACTCAGTGGCAATCT
Found at i:129839 original size:27 final size:28
Alignment explanation
Indices: 129788--129846 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
129778 CATCTTTTTT
* **
129788 CCTTTTAAGTCCTACAACTTTGTGGCAC
1 CCTTTTAAGACCTACAACTCCGTGGCAC
*
129816 CCTTTTAAGACC-ACAACTCCGTGGCAT
1 CCTTTTAAGACCTACAACTCCGTGGCAC
129843 CCTT
1 CCTT
129847 GTTCCTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (28 bp):
CCTTTTAAGACCTACAACTCCGTGGCAC
Found at i:129854 original size:34 final size:34
Alignment explanation
Indices: 129816--129947 Score: 160
Period size: 34 Copynumber: 3.9 Consensus size: 34
129806 TTTGTGGCAC
*
129816 CCTTTTAAGACCACAACTCCGTGGCATCCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCCTTGTT
*
129850 CCTTTTAAGTCCACAACTCCATGGCATCCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCCTTGTT
* * *
129884 CCTTTTAAGTCTACGACTCTGTGGCAT-CTT-TCT
1 CCTTTTAAGTCCACAACTCCGTGGCATCCTTGT-T
* * * *
129917 CCTTTTAAGCCCACAAGTCAGTGGCACCCTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCCTT
129948 TTCAAAAGCC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 25 0.30
34 58 0.69
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (34 bp):
CCTTTTAAGTCCACAACTCCGTGGCATCCTTGTT
Found at i:129942 original size:67 final size:68
Alignment explanation
Indices: 129816--129947 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 68
129806 TTTGTGGCAC
* *
129816 CCTTTTAAGACCACAACTCCGTGGCATCCTTGTTCCTTTTAAGTCCACAACTCCATGGCATCCTT
1 CCTTTTAAGACCACAACTCCGTGGCATCCTTGTTCCTTTTAAGCCCACAACTCCATGGCACCCTT
129881 GTT
66 GTT
* * * * *
129884 CCTTTTAAGTCTACGACTCTGTGGCAT-CTT-TCTCCTTTTAAGCCCACAAGT-CAGTGGCACCC
1 CCTTTTAAGACCACAACTCCGTGGCATCCTTGT-TCCTTTTAAGCCCACAACTCCA-TGGCACCC
129946 TT
64 TT
129948 TTCAAAAGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
66 3 0.05
67 29 0.53
68 23 0.42
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (68 bp):
CCTTTTAAGACCACAACTCCGTGGCATCCTTGTTCCTTTTAAGCCCACAACTCCATGGCACCCTT
GTT
Found at i:130021 original size:28 final size:30
Alignment explanation
Indices: 129923--130048 Score: 161
Period size: 30 Copynumber: 4.3 Consensus size: 30
129913 TTCTCCTTTT
129923 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
129953 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
* *
129983 AAGCCCACAAGTCAATGGCAACC-TTT-AA
1 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
* ** *
130011 AAGCACACAAGTTGGT-GCAACCC-CTTCAA
1 AAGCCCACAAGTCAGTGGC-ACCCTTTTCAA
130040 AAGCCCACA
1 AAGCCCACA
130049 CAAGTTGGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
27 2 0.02
28 19 0.22
29 13 0.15
30 51 0.60
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.17
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCTTTTCAA
Found at i:130306 original size:101 final size:101
Alignment explanation
Indices: 130071--130946 Score: 1355
Period size: 101 Copynumber: 8.8 Consensus size: 101
130061 GTCTTCTTCC
* * * * *
130071 AAGTCCAATATTGCTGGCCTTGAACCAGCATATTGGC-ACATTG---TCTTTAAGACCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
130132 CTGGCCTTGAATCAGCACATTGGCA----C--CTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
130162 AAGTCCAATATCGCTGGCCTTGAAGT-AGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTC
1 AAGTCCAATATCGCTGGCCTTGAA-TCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTC
*
130226 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTT
65 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
*
130263 AAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
* * *
130328 CTAGCCTTGAATCAGCATATTGGCACCATCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
* * * *
130364 AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTTAAATCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
130429 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
* ** *
130465 AAGTCCAATATCACTACCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCA
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
130530 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
*
130566 AAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
* * *
130631 TTAGCCTTGAATCAGTACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
* * *
130667 AAGTCCAATATCGCTGGCCTTAAATCAGCATCTTGGCGCCTTTGCCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
130732 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
*
130768 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCATTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
130833 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
* * * * *
130869 AAGACCAGTATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTTTCATC-TTAAGGCCAATGTC-
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
*
130932 CACGGCCTTGAATCA
66 C-TGGCCTTGAATCA
130947 TCGCCTGGCC
Statistics
Matches: 723, Mismatches: 49, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
91 34 0.05
92 4 0.01
95 41 0.06
99 2 0.00
100 26 0.04
101 616 0.85
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (101 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
Found at i:130414 original size:202 final size:198
Alignment explanation
Indices: 130071--132282 Score: 2441
Period size: 202 Copynumber: 10.9 Consensus size: 198
130061 GTCTTCTTCC
* * * * * * *
130071 AAGTCCAATATTGCTGGCCTTGAACCAGCATATTGGCACATT-GTCTTTAAGACCAATGTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* *
130135 GCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAAGT-AGCAT
66 GCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATATCGCTGGCCTTGAA-TCAGCAC
* * *
130193 ATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-T-T
130 ATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTGT
130256 CATCTTT
192 CATCTTT
* * * *
130263 AAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCG
* * *
130328 CTAGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGC
63 CTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* * * * *
130393 ATATTGGCACCTTTTTCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T
128 ACATTGGCACC---TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
130457 -TCATCTTT
190 GTCATCTTT
* ** * * * *
130465 AAGTCCAATATCACTACCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCA
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCG
* * *
130530 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGC
63 CTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* * * * * * * *
130595 ATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGTTAGCCTTGAATCAGTACATTGGCACC-T
128 ACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
130659 -TCATCTTT
190 GTCATCTTT
* * *
130667 AAGTCCAATATCGCTGGCCTTAAATCAGCATC-TTGGCGCCTTTGCCATCTTTAAGTCCAATGTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCA-CATTGGCACC-TT--CATCTTTAAGTCCAATATC
* *
130731 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
62 GCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
* * * * *
130796 CATATTGGCGCCATTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-
127 CACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCT
130860 T-TCATCTTT
189 TGTCATCTTT
* * * * * *
130869 AAGACCAGTATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTTTCATCTTAAGGCCAATGTCCA
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC---TTCATCTT-----TAA-GT---
*
130934 CGGCCTTGAATCATCGCCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTTTAA-TCCAAT
54 ---CC---AAT-ATCG-CTGGCCTTGAATCAGCATATTGGCAC---CGTCATCTTTAAGTCCAAT
* * *
130998 GTTCGCT-GCCTT-AATC-GCAAATTGGCACCTTCATCTTTAAGTCCAATATCGTTTGGCCTTG-
108 -ATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG-CTGGCCTTGA
*
131059 ATCAGCATATTGGGTGCCTTGTCATCTTT
171 ATCAGCATATT-GGCGCCTTGTCATCTTT
* * *
131088 AAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATTTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
** *
131153 GTTTTGAATCAGCATATTGGCACCGTCATCTTTTCAAGT-CAATTGTCGCTGGCCTTGAATCA-C
66 GCCTTGAATCAGCATATTGGCACCGTCATC-TTT-AAGTCCAA-TATCGCTGGCCTTGAATCAGC
* *
131216 ACATCGGCACCTTCAATCTTTAAGTGCCAATATCTCTGGCCTTG-ATCAGCATATTGGCCGCCTT
128 ACATTGGCACCTTC-ATCTTTAAGT-CCAATATCGCTGGCCTTGAATCAGCATATTGG-CGCC-T
131280 TGTCATCTTT
189 TGTCATCTTT
* *
131290 AAGTCCAATGTCGCTGG-CTTG-ATCAGCACATTGGCA-CTTCATCTTTAAGTCCAAGTATCACT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA-TATCGCT
* * *
131352 GGCCTTGAATCAGCATATTGGCGCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
65 GGCCTTGAATCAGCATATTGGCAC--CGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
131417 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGT
128 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGT
131482 CATCTTT
192 CATCTTT
* * *
131489 AAGTCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* * * * *
131554 GCCTTGAATTAGCATATTGGCGCTTTTGTCATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGC
66 GCCTTGAATCAGCATATTGGCAC---CGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
131619 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGT
128 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGT
131684 CATCTTT
192 CATCTTT
* *
131691 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* ** *
131756 GCCTTGAATCAGCATATTGGCGCTTTTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
66 GCCTTGAATCAGCATATTGGCAC---CGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* ** * *
131821 ACATCGGCACCTTCATCTTTAAGTCCAATATCTTTGGCCTTGAATCAGCATATTGGTGCCTTTAT
128 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGT
131886 CATCTTT
192 CATCTTT
*
131893 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* *
131958 GCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
66 GCCTTGAATCAGCATATTGGCACC---GTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
132023 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGT
128 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGT
132088 CATCTTT
192 CATCTTT
* * *
132095 AAGTCCAA-AGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTATCGCT
1 AAGTCCAATA-TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* ** * * *
132159 GGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTC-ATGGCCTTAAATCA
65 GGCCTTGAATCAGCATATTGGC-AC--CGTCATCTTT-AAGTCCAATATCGCTGGCCTTGAATCA
* * * * * * *
132223 GCACATTGGCATTCTTCTCATCTTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTG
126 GCACATTGGCA--CCT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
132283 ACATCCTTTT
Statistics
Matches: 1820, Mismatches: 124, Indels: 139
0.87 0.06 0.07
Matches are distributed among these distances:
192 35 0.02
194 1 0.00
195 1 0.00
196 46 0.03
197 3 0.00
198 10 0.01
199 98 0.05
200 114 0.06
201 108 0.06
202 1171 0.64
203 14 0.01
204 7 0.00
205 37 0.02
207 2 0.00
208 2 0.00
210 2 0.00
211 2 0.00
214 2 0.00
216 38 0.02
217 16 0.01
218 4 0.00
219 77 0.04
220 4 0.00
221 11 0.01
222 15 0.01
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (198 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
GCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACA
TTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATC
TTT
Found at i:130608 original size:303 final size:295
Alignment explanation
Indices: 130071--132282 Score: 2397
Period size: 303 Copynumber: 7.3 Consensus size: 295
130061 GTCTTCTTCC
* * * * * * *
130071 AAGTCCAATATTGCTGGCCTTGAACCAGCATATTGGCACATT-GTCTTTAAGACCAATGTCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* *
130135 GCCTTGAATCAGCACATT---G---G-CACCTTTAAGTCCAATATCGCTGGCCTTGAAGT-AGCA
66 GCCTTGAATCAGCACATTGGCGCCTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAA-TCAGCA
* * *
130192 TATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTC
130 CATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
* * *
130257 ATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCA
192 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCA
* *
130322 ATGTCGCTAGCCTTGAATCAGCATATTGGCACCATCATCTTT
254 ATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTT
* * * *
130364 AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTTAAATCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC---TTCATCTTTAAGTCCAATATCG
* * * **
130429 CTGGCCTTGAATCAGCACATTGGCACCT-TCATCTTTAAGTCCAATATCACTACCCTTGAATCAG
63 CTGGCCTTGAATCAGCACATTGGCGCCTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAG
* * * * *
130493 CATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCT
128 CACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
* * *
130558 TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTC
190 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTC
* * * * * *
130623 CAATGTCGTTAGCCTTGAATCAGTACATTGGCACCTTCATCTTT
252 CAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTT
* * *
130667 AAGTCCAATATCGCTGGCCTTAAATCAGCATC-TTGGCGCCTTTGCCATCTTTAAGTCCAATGTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCA-CATTGGCACC-TT--CATCTTTAAGTCCAATATC
* *
130731 GCTGGCCTTGAATCAGCACATTGGCACCT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
62 GCTGGCCTTGAATCAGCACATTGGCGCCTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCA
* * * *
130795 GCATATTGGCGCCATTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
127 GCACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
* * * * *
130860 TTCATCTTTAAGACCAGTATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTTTCATCTTAAGGC
189 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC---TTCATCTT-----
*
130925 CAATGTCCACGGCCTTGAATCATCGCCTGGCCTTGAATCAGCATATTGGCA-CATTTGTCATCTT
246 TAA-GT------CC---AAT-ATCG-CTGGCCTTGAATCAGCATATTGGCACCA----TCATCTT
130989 T
295 T
* * *
130990 AA-TCCAATGTTCGCT-GCCTT-AATC-GCAAATTGGCACCTTCATCTTTAAGTCCAATATCGTT
1 AAGTCCAAT-ATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG-C
* * *
131051 TGGCCTTG-ATCAGCATATTGGGTGCCTTGTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCA
64 TGGCCTTGAATCAGCACATT-GGCGCC-TGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCA
* ** *
131115 GCACATTGGCACCTTCATCTTTAAGTCCAATTTCGCTGGTTTTGAATCAGCATATTGGCACCGTC
127 GCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
* *
131180 ATCTTTTCAAGT-CAATTGTCGCTGGCCTTGAATCA-CACATCGGCACCTTCAATCTTTAAGTGC
192 ATC-TTT-AAGTCCAA-TATCGCTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTTTAAGT-C
* * *
131243 CAATATCTCTGGCCTTG-ATCAGCATATTGGCCGCCTTTGTCATCTTT
252 CAATATCGCTGGCCTTGAATCAGCATATTGG-CACC---ATCATCTTT
* *
131290 AAGTCCAATGTCGCTGG-CTTG-ATCAGCACATTGGCA-CTTCATCTTTAAGTCCAAGTATCACT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA-TATCGCT
* *
131352 GGCCTTGAATCAGCATATTGGCGCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
65 GGCCTTGAATCAGCACATTGGCGC-CTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
**
131417 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGT
129 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-T
* *
131482 CATCTTTAAGTCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
191 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* * * **
131547 ATCGTTGGCCTTGAATTAGCATATTGGCGCTTTTGTCATCTTT
256 ATCGCTGGCCTTGAATCAGCATATTGGCAC---CATCATCTTT
* *
131590 AAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* *
131655 GCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
66 GCCTTGAATCAGCACATTGGCGCC--TGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
* * *
131720 ACATTGACACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCTTTTTT
129 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC---CTT
* *
131785 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTCATCTTTAAGTCCAAT
191 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
** **
131850 ATCTTTGGCCTTGAATCAGCATATTGGTGCCTTTATCATCTTT
256 ATCGCTGGCCTTGAATCAGCATATTGGCACC---ATCATCTTT
*
131893 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
*
131958 GCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
66 GCCTTGAATCAGCACATTGGCGCC--TGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
* *
132023 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGT
129 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-T
* * *
132088 CATCTTTAAGTCCAA-AGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAG
191 CATCTTTAAGTCCAATA-TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* *
132152 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTT
255 TATCGCTGGCCTTGAATCAGCATATTGGC-AC--CATCATCTTT
** * * * * * * *
132196 AAAACCCAATGTC-ATGGCCTTAAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCTAATGTC
1 -AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCATCTTTAAGTCCAATATC
* *
132260 GCTGACCGTGAATCAGCACATTG
62 GCTGGCCTTGAATCAGCACATTG
132283 ACATCCTTTT
Statistics
Matches: 1705, Mismatches: 124, Indels: 167
0.85 0.06 0.08
Matches are distributed among these distances:
293 38 0.02
296 2 0.00
297 37 0.02
299 13 0.01
300 198 0.12
301 87 0.05
302 69 0.04
303 945 0.55
304 15 0.01
305 5 0.00
306 38 0.02
308 2 0.00
309 2 0.00
310 2 0.00
311 2 0.00
315 5 0.00
316 5 0.00
317 78 0.05
318 29 0.02
319 28 0.02
320 75 0.04
321 4 0.00
322 11 0.01
323 15 0.01
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (295 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
GCCTTGAATCAGCACATTGGCGCCTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCAC
ATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCT
TTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
TGGCCTTGAATCAGCATATTGGCACCATCATCTTT
Found at i:131164 original size:101 final size:100
Alignment explanation
Indices: 130946--132282 Score: 1946
Period size: 101 Copynumber: 13.3 Consensus size: 100
130936 GCCTTGAATC
* *
130946 ATCGCCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTTTAA-TCCAATGTTCGCT-GCCT
1 ATCG-CTGGCCTTGAATCAGCATATTGGCGC-CTTGTCATCTTTAAGTCCAATG-TCGCTGGCCT
*
131009 T-AATC-GCAAATTGGCACCTTCATCTTTAAGTCCAAT
63 TGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* * *
131045 ATCGTTTGGCCTTG-ATCAGCATATTGGGTGCCTTGTCATCTTTAAGTCCAATGTCGCTAGCCTT
1 ATCG-CTGGCCTTGAATCAGCATATT-GGCGCCTTGTCATCTTTAAGTCCAATGTCGCTGGCCTT
131109 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
64 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* ** *
131146 TTCGCTGGTTTTGAATCAGCATATTGGCACC--GTCATCTTTTCAAGT-CAATTGTCGCTGGCCT
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATC-TTT-AAGTCCAA-TGTCGCTGGCCT
*
131208 TGAATCA-CACATCGGCACCTTCAATCTTTAAGTGCCAAT
63 TGAATCAGCACATTGGCACCTTC-ATCTTTAAGT-CCAAT
*
131247 ATCTCTGGCCTTG-ATCAGCATATTGGCCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGG-CTT
1 ATCGCTGGCCTTGAATCAGCATATTGG-CGCC-TTGTCATCTTTAAGTCCAATGTCGCTGGCCTT
131310 G-ATCAGCACATTGGCA-CTTCATCTTTAAGTCCAAGT
64 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA-T
* *
131346 ATCACTGGCCTTGAATCAGCATATTGGCGCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
131411 ATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
66 ATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* *
131446 ATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTA
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
131511 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* * * *
131547 ATCGTTGGCCTTGAATTAGCATATTGGCGCTTTTGTCATCTTTAAGTCCAATGTCGTTGGCCTTG
1 ATCGCTGGCCTTGAATCAGCATATTGGCGC-CTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
131612 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
*
131648 ATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
*
131713 AATCAGCACATTGACACCTTCATCTTTAAGTCCAAT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* *
131749 ATCGCTGGCCTTGAATCAGCATATTGGCGCTTTTTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
1 ATCGCTGGCCTTGAATCAGCATATTGGCGC-CTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
*
131814 AATCAGCACATCGGCACCTTCATCTTTAAGTCCAAT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
** * *
131850 ATCTTTGGCCTTGAATCAGCATATTGGTGCCTTTATCATCTTTAAGTCCAATGTCGCTGGCCTTG
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
131915 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
131951 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
132016 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
* * *
132052 ATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAAGTCGCTAGCCTTG
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTTTAAGTCCAATGTCGCTGGCCTTG
* *
132117 AATCAGCACATTGGCACCTTCATCTTTAAGACCAGT
65 AATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
** *
132153 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTC-ATGGCCTT
1 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTT-GTCATCTTT-AAGTCCAATGTCGCTGGCCTT
* * * *
132217 AAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCTAAT
64 GAATCAGCACATTGGCA--CCT-TCATCTTTAAGTCCAAT
* * * *
132257 GTCGCTGACCGTGAATCAGCACATTG
1 ATCGCTGGCCTTGAATCAGCATATTG
132283 ACATCCTTTT
Statistics
Matches: 1132, Mismatches: 74, Indels: 59
0.89 0.06 0.05
Matches are distributed among these distances:
98 67 0.06
99 77 0.07
100 126 0.11
101 791 0.70
102 22 0.02
103 8 0.01
104 41 0.04
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (100 bp):
ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
ATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
Found at i:133033 original size:19 final size:18
Alignment explanation
Indices: 132986--133101 Score: 83
Period size: 19 Copynumber: 6.7 Consensus size: 18
132976 ATTTCAACAA
*
132986 TTTGTATCGATACAAACTAG
1 TTTGTATCGATACATA--AG
133006 TAATTGTATCGATACATAAG
1 T--TTGTATCGATACATAAG
133026 TGTTGTATCGATAC---A-
1 T-TTGTATCGATACATAAG
133041 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
133057 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
133073 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
133089 TTTTGTATCGATA
1 -TTTGTATCGATA
133102 TAATGTATCG
Statistics
Matches: 79, Mismatches: 2, Indels: 31
0.71 0.02 0.28
Matches are distributed among these distances:
12 11 0.14
13 11 0.14
15 3 0.04
16 1 0.01
17 2 0.03
19 33 0.42
20 4 0.05
22 14 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:133046 original size:12 final size:12
Alignment explanation
Indices: 133029--133053 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
133019 ACATAAGTGT
133029 TGTATCGATACA
1 TGTATCGATACA
133041 TGTATCGATACA
1 TGTATCGATACA
133053 T
1 T
133054 AAGTGTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:133078 original size:13 final size:13
Alignment explanation
Indices: 133060--133084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
133050 ACATAAGTGT
133060 TGTATCGATACAA
1 TGTATCGATACAA
133073 TGTATCGATACA
1 TGTATCGATACA
133085 TAAGTTTTGT
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:133081 original size:32 final size:32
Alignment explanation
Indices: 133010--133111 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
133000 AACTAGTAAT
133010 TGTATCGATACATAAGTGTTGTATCGATAC-A
1 TGTATCGATACATAAGTGTTGTATCGATACAA
133041 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
133073 TGTATCGATACATAAGTTTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
133105 TGTATCG
1 TGTATCG
133112 CTACGAAGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 30 0.44
32 38 0.56
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:139215 original size:17 final size:16
Alignment explanation
Indices: 139190--139228 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
139180 AAGAAGCTAA
*
139190 TTAAGTTATCACTATTT
1 TTAATTTATCA-TATTT
*
139207 TTAATTTATTATATTT
1 TTAATTTATCATATTT
139223 TTAATT
1 TTAATT
139229 AATTATGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAATTTATCATATTT
Found at i:139223 original size:16 final size:16
Alignment explanation
Indices: 139202--139234 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
139192 AAGTTATCAC
*
139202 TATTTTTAATTTATTA
1 TATTTTTAATTAATTA
139218 TATTTTTAATTAATTA
1 TATTTTTAATTAATTA
139234 T
1 T
139235 GCTTTAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTAATTAATTA
Found at i:139366 original size:2 final size:2
Alignment explanation
Indices: 139359--139399 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
139349 ACAATCTATC
139359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
139400 TCTTTGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:141304 original size:132 final size:129
Alignment explanation
Indices: 141048--141384 Score: 473
Period size: 132 Copynumber: 2.7 Consensus size: 129
141038 ACTATTTTTT
* * * *
141048 AATAATAAATAATATTTAATTAAATTTAAAAAAATTTACATTAATAAACT-AAA-A-T-ATTA--
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAAA-TTACATTAACAAATTAAAATATTAATTATT
141107 AT-TTTTT-TAAAATTAAAAAATTTAAATAAAAAATAAAAAGGGTTTATTATTATTTTTTAATAA
65 ATGTTTTTATAAAATTAAAAAATTTAAATAAAAAATAAAAAGGGTTTATTATTATTTTTTAATAA
*
141170 AATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTA
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTA
141235 TGTTTTTATAAAATTAAAAAATTTTAAAATAAAAAATAAAAA-GGTTT-TTAATTATAATTTTTA
66 TGTTTTTATAAAATTAAAAAA-TTT-AAATAAAAAATAAAAAGGGTTTATT-ATTAT--TTTTTA
141298 ATAA
126 ATAA
* *
141302 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAGTATTAATTATTA
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTA
141367 TGTTTTTA-AAAA-TAAAAA
66 TGTTTTTATAAAATTAAAAA
141385 GTATTTATTA
Statistics
Matches: 194, Mismatches: 8, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
121 13 0.07
122 34 0.18
123 1 0.01
124 1 0.01
125 4 0.02
127 2 0.01
128 5 0.03
129 15 0.08
130 19 0.10
131 20 0.10
132 80 0.41
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (129 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTA
TGTTTTTATAAAATTAAAAAATTTAAATAAAAAATAAAAAGGGTTTATTATTATTTTTTAATAA
Found at i:141383 original size:108 final size:108
Alignment explanation
Indices: 141266--141461 Score: 283
Period size: 108 Copynumber: 1.8 Consensus size: 108
141256 TTTTAAAATA
*
141266 AAAAATAAAAAGGT-TTT-TAATTATAA-TTTTTAATAAAATAAAAAATAATATTTAATT-AAGT
1 AAAAATAAAAA-GTATTTATAATTATAATTTTTTAAT--AAGAAAAAATAATATTTAATTAAAGT
141327 TTAAAAAATTTACATTAACAAATTAAAGTATTAATTATTATGTTTTT
63 TTAAAAAA-TTACATTAACAAATTAAAGTATTAATTATTATGTTTTT
* * *
141374 AAAAATAAAAAGTATTTATTATTATTATTTTTTAATAAGAAAAAATAATATTTAATTAAATTTTA
1 AAAAATAAAAAGTATTTATAATTATAATTTTTTAATAAGAAAAAATAATATTTAATTAAAGTTTA
*
141439 AAAAATTATATTAACAAATTAAA
66 AAAAATTACATTAACAAATTAAA
141462 AAATAATATT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
107 2 0.03
108 51 0.65
109 18 0.23
110 8 0.10
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (108 bp):
AAAAATAAAAAGTATTTATAATTATAATTTTTTAATAAGAAAAAATAATATTTAATTAAAGTTTA
AAAAATTACATTAACAAATTAAAGTATTAATTATTATGTTTTT
Found at i:141462 original size:21 final size:21
Alignment explanation
Indices: 141436--141509 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
141426 TAATTAAATT
141436 TTAAAAAATTATATTAACAAA
1 TTAAAAAATTATATTAACAAA
* *
141457 TTAAAAAATAATATTTAAGAAA
1 TTAAAAAATTATA-TTAACAAA
*
141479 TTAAAAAAATTATCATTATTCAAA
1 TT-AAAAAATTAT-ATTA-ACAAA
141503 -TAAAAAA
1 TTAAAAAA
141510 CTCTCTATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 12 0.27
22 15 0.34
23 13 0.30
24 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (21 bp):
TTAAAAAATTATATTAACAAA
Found at i:141474 original size:22 final size:22
Alignment explanation
Indices: 141413--141486 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
141403 TTTTAATAAG
*
141413 AAAAAATAATATTTAATTAAATTTT
1 AAAAAATAATATTTAA-CAAA--TT
*
141438 AAAAAATTATA-TTAACAAATT
1 AAAAAATAATATTTAACAAATT
*
141459 AAAAAATAATATTTAAGAAATT
1 AAAAAATAATATTTAACAAATT
141481 AAAAAA
1 AAAAAA
141487 ATTATCATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 12 0.27
22 15 0.34
23 3 0.07
24 4 0.09
25 10 0.23
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (22 bp):
AAAAAATAATATTTAACAAATT
Found at i:141486 original size:108 final size:107
Alignment explanation
Indices: 141264--141486 Score: 249
Period size: 108 Copynumber: 2.1 Consensus size: 107
141254 AATTTTAAAA
*
141264 TAAAAAATAAAAAGGTTTTTAATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAAGTTT
1 TAAAAAATAAAAAGGTTTTTAATTATAATTTTTAAT-AAAGAAAAAATAATATTTAATTAAGTTT
* * * **
141329 AAAAAATTTACATTAACAAATTAAAGTATTAATTATTATGTTT
65 AAAAAATTTACATTAACAAATTAAAGAAATAATTATTAAGAAT
* * * *
141372 TTAAAAATAAAAA-GTATTTATTATTATTATTTTTTAAT-AAGAAAAAATAATATTTAATTAAAT
1 TAAAAAATAAAAAGGT-TTT-TAATTA-TAATTTTTAATAAAGAAAAAATAATATTTAATT-AAG
*
141435 TTTAAAAAA-TTATATTAACAAATTAAA-AAATAA-TATTTAAGAAAT
62 TTTAAAAAATTTACATTAACAAATTAAAGAAATAATTA-TTAAG-AAT
141480 TAAAAAA
1 TAAAAAA
141487 ATTATCATTA
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
106 2 0.02
107 10 0.10
108 59 0.61
109 16 0.16
110 10 0.10
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (107 bp):
TAAAAAATAAAAAGGTTTTTAATTATAATTTTTAATAAAGAAAAAATAATATTTAATTAAGTTTA
AAAAATTTACATTAACAAATTAAAGAAATAATTATTAAGAAT
Found at i:141507 original size:45 final size:46
Alignment explanation
Indices: 141413--141509 Score: 128
Period size: 46 Copynumber: 2.1 Consensus size: 46
141403 TTTTAATAAG
* *
141413 AAAAAATAATATTTAATTAAATTTTAAAAAATTATATTAACAAATT
1 AAAAAATAATATTTAATGAAATTTAAAAAAATTATATTAACAAATT
*
141459 AAAAAATAATATTTAA-GAAA-TTAAAAAAATTATCATTATTCAAA-T
1 AAAAAATAATATTTAATGAAATTTAAAAAAATTAT-ATTA-ACAAATT
141504 AAAAAA
1 AAAAAA
141510 CTCTCTATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
44 12 0.26
45 14 0.30
46 20 0.43
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (46 bp):
AAAAAATAATATTTAATGAAATTTAAAAAAATTATATTAACAAATT
Found at i:144339 original size:13 final size:13
Alignment explanation
Indices: 144321--144346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
144311 ACATTTCACC
144321 ATGTATCGATACA
1 ATGTATCGATACA
144334 ATGTATCGATACA
1 ATGTATCGATACA
144347 CTATATCAAT
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:144431 original size:19 final size:20
Alignment explanation
Indices: 144385--144456 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
144375 CTCCTAGTTT
*
144385 CATGTATCGATAC-AATTCAA
1 CATGTATCGATACTAAGT-AA
** *
144405 TGTGTATCGATACTATG-AA
1 CATGTATCGATACTAAGTAA
144424 CATGTATCGATACTAAGTAA
1 CATGTATCGATACTAAGTAA
*
144444 TATGTATCGATAC
1 CATGTATCGATAC
144457 ATCTGGGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.38
20 25 0.60
21 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACTAAGTAA
Found at i:152242 original size:15 final size:14
Alignment explanation
Indices: 152210--152257 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
152200 ATATTAAATA
*
152210 ATTAAATGAATATTT
1 ATTAAAT-ATTATTT
152225 ATTAAATATTATTAT
1 ATTAAATATTATT-T
*
152240 ATTTAATATTCATTT
1 ATTAAATATT-ATTT
152255 ATT
1 ATT
152258 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.72
16 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTAAATATTATTT
Found at i:152258 original size:15 final size:14
Alignment explanation
Indices: 152220--152273 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
152210 ATTAAATGAA
*
152220 TATTTATTAAATAT
1 TATTTATTTAATAT
152234 TATTATATTTAATAT
1 TATT-TATTTAATAT
*
152249 TCATTTATTTTTAAAAT
1 T-ATTTA--TTTAATAT
152266 TATTTATT
1 TATTTATT
152274 CATTGTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 6 0.18
15 12 0.35
16 8 0.24
17 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTATTTAATAT
Found at i:152261 original size:17 final size:16
Alignment explanation
Indices: 152220--152273 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
152210 ATTAAATGAA
152220 TATTTATTAAATATTA-T
1 TATTT-TTAAA-ATTATT
* *
152237 TATATTTAATATTCATT
1 TATTTTTAAAATT-ATT
152254 TATTTTTAAAATTATT
1 TATTTTTAAAATTATT
152270 TATT
1 TATT
152274 CATTGTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 3 0.10
16 12 0.39
17 16 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAAAATTATT
Found at i:152782 original size:13 final size:13
Alignment explanation
Indices: 152764--152790 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
152754 CACTGACAGC
152764 AAGTAAAACGCGT
1 AAGTAAAACGCGT
152777 AAGTAAAACGCGT
1 AAGTAAAACGCGT
152790 A
1 A
152791 GGACTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (13 bp):
AAGTAAAACGCGT
Found at i:153087 original size:17 final size:17
Alignment explanation
Indices: 153067--153121 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
153057 ATAATATAAC
*
153067 TAAATATATATTTTTAT
1 TAAATATTTATTTTTAT
* *
153084 TAAAAATTTA-TTATAT
1 TAAATATTTATTTTTAT
*
153100 TTAATATTTATTTATTAT
1 TAAATATTTATTT-TTAT
153118 TAAA
1 TAAA
153122 ATCACTTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 13 0.45
17 10 0.34
18 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATATTTATTTTTAT
Found at i:153132 original size:31 final size:33
Alignment explanation
Indices: 153097--153159 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
153087 AAATTTATTA
153097 TATTTAATATTTA-TTTATTAT-TAAAATCACT
1 TATTTAATATTTATTTTATTATATAAAATCACT
* *
153128 TATTTAATGTTTATTTTTTTATATAAAATCAC
1 TATTTAATATTTATTTTATTATATAAAATCAC
153160 CAAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.43
32 7 0.25
33 9 0.32
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (33 bp):
TATTTAATATTTATTTTATTATATAAAATCACT
Found at i:153636 original size:20 final size:19
Alignment explanation
Indices: 153611--153681 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
153601 ATTTTAAAAA
153611 ATATTTAATTAATTAATAT
1 ATATTTAATTAATTAATAT
153630 GATATTT-A-TAA-TAATA-
1 -ATATTTAATTAATTAATAT
*
153646 ATATTATTATTAATTAAATAT
1 ATATT-TAATTAATT-AATAT
*
153667 AATATTTAATAAATT
1 -ATATTTAATTAATT
153682 TTTTTATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
15 5 0.12
16 1 0.02
17 6 0.14
18 6 0.14
19 2 0.05
20 10 0.24
21 7 0.17
22 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
ATATTTAATTAATTAATAT
Found at i:161356 original size:25 final size:25
Alignment explanation
Indices: 161325--161379 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
161315 GAAAGTAATG
* *
161325 TTAAAAAATTAATAAAAAGAAAATTT
1 TTAAAACA-TAATAAAAAGAAAATTC
*
161351 TTAAAACATAATAAAATGAAAATTC
1 TTAAAACATAATAAAAAGAAAATTC
161376 TTAA
1 TTAA
161380 GTTATCCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (25 bp):
TTAAAACATAATAAAAAGAAAATTC
Found at i:162948 original size:13 final size:13
Alignment explanation
Indices: 162930--162954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162920 CATAAAGTAT
162930 TGTATCGATACAA
1 TGTATCGATACAA
162943 TGTATCGATACA
1 TGTATCGATACA
162955 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:162970 original size:32 final size:33
Alignment explanation
Indices: 162910--162978 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
162900 TTCAACGATT
162910 TGTATCAATACATAAAGTATTGTATCGATACAA
1 TGTATCAATACATAAAGTATTGTATCGATACAA
* *
162943 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1 TGTATCAATACATAAAGTATTGTATCGATACAA
162975 TGTA
1 TGTA
162979 AGCTACTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (33 bp):
TGTATCAATACATAAAGTATTGTATCGATACAA
Found at i:163034 original size:13 final size:13
Alignment explanation
Indices: 163016--163040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163006 ATTACTCAAA
163016 TGTATCGATACAT
1 TGTATCGATACAT
163029 TGTATCGATACA
1 TGTATCGATACA
163041 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:163092 original size:52 final size:52
Alignment explanation
Indices: 163049--163229 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
163039 CACTGATCTT
*
163049 TGTATAGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
163101 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
163153 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
163205 TGTATCGATATATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
163230 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:166356 original size:10 final size:10
Alignment explanation
Indices: 166341--166378 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
166331 CCAATTTGAA
166341 TTATCTTATT
1 TTATCTTATT
166351 TTATCTTATT
1 TTATCTTATT
*
166361 TGA--TTATT
1 TTATCTTATT
166369 TTATCTTATT
1 TTATCTTATT
166379 CGATCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 7 0.29
10 17 0.71
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (10 bp):
TTATCTTATT
Found at i:167873 original size:29 final size:29
Alignment explanation
Indices: 167828--167884 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
167818 GTTATTAAGC
*
167828 CCTTAAACTTTTTAAAATTACACTTTGAT
1 CCTTAAACTTTTCAAAATTACACTTTGAT
167857 CCTTAAACTTTTCAAAATTACACTTTGA
1 CCTTAAACTTTTCAAAATTACACTTTGA
167885 CCCCAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (29 bp):
CCTTAAACTTTTCAAAATTACACTTTGAT
Found at i:169908 original size:15 final size:15
Alignment explanation
Indices: 169888--169926 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
169878 GATGAATTTT
*
169888 AAAAAATTTAAACTA
1 AAAAAATTTAAACCA
*
169903 AAAAAATAT-AACCA
1 AAAAAATTTAAACCA
169917 AAAAAATTTA
1 AAAAAATTTA
169927 TGGAGTAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAATTTAAACCA
Found at i:170427 original size:12 final size:11
Alignment explanation
Indices: 170410--170443 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
170400 CTAACTTTTT
170410 AAATTTTACAAA
1 AAATTTTA-AAA
170422 AAATTTT-AAA
1 AAATTTTAAAA
170432 AAATTTTAAAA
1 AAATTTTAAAA
170443 A
1 A
170444 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 4 0.19
12 7 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTTTAAAA
Found at i:171889 original size:66 final size:67
Alignment explanation
Indices: 171775--172092 Score: 236
Period size: 66 Copynumber: 4.8 Consensus size: 67
171765 ACAAAGACGA
* * ** * *
171775 AACCTAAGTC-AAAAAAGAGTTGACAAAGGTGAAACCAATAAAGTTAACTAAAAGAGATTAAGGC
1 AACCTAAGTCGAAAAAAGAGTTGACCAGGGCAAAACCGATAAAGTTAACTAAAAGAGACTAAGGC
171839 AG
66 AG
* * ** *
171841 ACCCTAAGTCGAAAAAAGAGTTGACTAGGGCAAAATTGATAAA-TTAACTAAGCAA-A-ACTAGG
1 AACCTAAGTCGAAAAAAGAGTTGACCAGGGCAAAACCGATAAAGTTAACTAA--AAGAGACTAAG
*
171903 GCGG
64 GCAG
* ** * * * * * * *
171907 AACCTAAGTCGGAAAGGGTGTTGACTAGAGCGAAACCGATAAAATCAACTGAAAGAGACTAAGGC
1 AACCTAAGTCGAAAAAAGAGTTGACCAGGGCAAAACCGATAAAGTTAACTAAAAGAGACTAAGGC
171972 A-
66 AG
* * * * *
171973 AACTTAAGTC-AAAAAAGGTGTTGACCAGGGTAAAATCGATAAAGTTAACTAAAAGAGACTAGGG
1 AACCTAAGTCGAAAAAA-GAGTTGACCAGGGCAAAACCGATAAAGTTAACTAAAAGAGACTAAGG
**
172037 TGG
65 CAG
** * * **
172040 AATTTAAGTCGAAAAAA-ATGTTGACCAGAGCAAAACTGATAAACCTAACTAAA
1 AACCTAAGTCGAAAAAAGA-GTTGACCAGGGCAAAACCGATAAAGTTAACTAAA
172093 TAGGATGTGG
Statistics
Matches: 195, Mismatches: 47, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
65 5 0.03
66 106 0.54
67 76 0.39
68 8 0.04
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (67 bp):
AACCTAAGTCGAAAAAAGAGTTGACCAGGGCAAAACCGATAAAGTTAACTAAAAGAGACTAAGGC
AG
Found at i:172034 original size:133 final size:132
Alignment explanation
Indices: 171775--172082 Score: 304
Period size: 133 Copynumber: 2.3 Consensus size: 132
171765 ACAAAGACGA
* * * * * *
171775 AACCTAAGTC-AAAAAAGA-GTTGA-CAAAGGTGAAACCAATAAAGTTAACTAAAAGAGATTAAG
1 AACCTAAGTCGAAAAAA-ATGTTGACCAGA-GCGAAACCGATAAAATCAACTAAAAGAGACTAAG
* * *
171837 GCAGACCCTAAGTCGAAAAAAGAGTTGACTAGGGCAAAATTGATAAATTAACTAAGCAAAACTAG
64 GCAGAACCTAAGTCGAAAAAAGAGTTGACCAGGGCAAAATCGATAAATTAACTAA-CAAAACTAG
171902 GGCGG
128 GGCGG
* *** * *
171907 AACCTAAGTCGGAAAGGGTGTTGACTAGAGCGAAACCGATAAAATCAACTGAAAGAGACTAAGGC
1 AACCTAAGTCGAAAAAAATGTTGACCAGAGCGAAACCGATAAAATCAACTAAAAGAGACTAAGGC
* * *
171972 A-AACTTAAGTC-AAAAAAGGTGTTGACCAGGGTAAAATCGATAAAGTTAACTAA-AAGAGACTA
66 AGAACCTAAGTCGAAAAAA-GAGTTGACCAGGGCAAAATCGATAAA-TTAACTAACAA-A-ACTA
*
172034 GGGTGG
127 GGGCGG
** * *
172040 AATTTAAGTCGAAAAAAATGTTGACCAGAGCAAAACTGATAAA
1 AACCTAAGTCGAAAAAAATGTTGACCAGAGCGAAACCGATAAA
172083 CCTAACTAAA
Statistics
Matches: 141, Mismatches: 28, Indels: 13
0.77 0.15 0.07
Matches are distributed among these distances:
131 8 0.06
132 41 0.29
133 90 0.64
134 2 0.01
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.18
Consensus pattern (132 bp):
AACCTAAGTCGAAAAAAATGTTGACCAGAGCGAAACCGATAAAATCAACTAAAAGAGACTAAGGC
AGAACCTAAGTCGAAAAAAGAGTTGACCAGGGCAAAATCGATAAATTAACTAACAAAACTAGGGC
GG
Found at i:172436 original size:67 final size:65
Alignment explanation
Indices: 172331--172556 Score: 186
Period size: 65 Copynumber: 3.4 Consensus size: 65
172321 AGAGTTGACC
* * *
172331 AGGGCTAAACTAATAAAGTTAACTAAAAAAATACTAGGGTGGAACCTAAGTCAAAAAAGGTATTG
1 AGGGCAAAACTGATAAAGTTAACT-AAAAAAGACTAGGGTGGAACCTAAGTC-AAAAAGGTATT-
172396 AT-T
63 -TCT
** * * * ** * * * *
172399 AGGGTGAAAGTGATGAAGTCAACTAAAAAAGACTAGGGCAGAACTTAAGTCGAAAGGGTGTTTCT
1 AGGGCAAAACTGATAAAGTTAACTAAAAAAGACTAGGGTGGAACCTAAGTCAAAAAGGTATTTCT
* * * * * *
172464 AGGGCAAAACTGATAAAGTTAACTAAAAGAGACTAGGGTGGAAACTAAGTCGAAAGGGTGTTGAC
1 AGGGCAAAACTGATAAAGTTAACTAAAAAAGACTAGGGTGGAACCTAAGTCAAAAAGGTATT-TC
172529 T
65 T
* *
172530 AGGACAAAACCT-ATAAAGCTAACTAAA
1 AGGGCAAAA-CTGATAAAGTTAACTAAA
172557 TAGGAGGTTG
Statistics
Matches: 129, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
64 1 0.01
65 53 0.41
66 32 0.25
67 25 0.19
68 18 0.14
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (65 bp):
AGGGCAAAACTGATAAAGTTAACTAAAAAAGACTAGGGTGGAACCTAAGTCAAAAAGGTATTTCT
Found at i:172497 original size:65 final size:67
Alignment explanation
Indices: 172409--172556 Score: 187
Period size: 65 Copynumber: 2.3 Consensus size: 67
172399 AGGGTGAAAG
* * * *
172409 TGATGAAGTCAACTAAAAAAGACTAGGGCAG-AACTTAAGTCGAAAGGGTGTT-TCTAGGGCAAA
1 TGATAAAGTTAACTAAAAAAGACTAGGGCAGAAAC-TAAGTCGAAAGGGTGTTGACTAGGACAAA
172472 A-C
65 ACC
* **
172474 TGATAAAGTTAACTAAAAGAGACTAGGGTGGAAACTAAGTCGAAAGGGTGTTGACTAGGACAAAA
1 TGATAAAGTTAACTAAAAAAGACTAGGGCAGAAACTAAGTCGAAAGGGTGTTGACTAGGACAAAA
172539 CC
66 CC
*
172541 T-ATAAAGCTAACTAAA
1 TGATAAAGTTAACTAAA
172557 TAGGAGGTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 43 0.60
66 27 0.38
67 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (67 bp):
TGATAAAGTTAACTAAAAAAGACTAGGGCAGAAACTAAGTCGAAAGGGTGTTGACTAGGACAAAA
CC
Done.