Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2031
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: 365977
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 3
Found at i:938 original size:19 final size:21
Alignment explanation
Indices: 904--943 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
894 TTTCCTGTTC
*
904 TGATTGTATCGATACA-ATTT
1 TGATTGTATAGATACATATTT
924 TGATTGT-TAGATACATATTT
1 TGATTGTATAGATACATATTT
944 GAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (21 bp):
TGATTGTATAGATACATATTT
Found at i:5788 original size:15 final size:15
Alignment explanation
Indices: 5768--5798 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5758 ATTTCGTTCG
*
5768 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5783 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5798 G
1 G
5799 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:9193 original size:32 final size:30
Alignment explanation
Indices: 9157--9215 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
9147 GAAAACAAGT
9157 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
9189 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
9216 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:9514 original size:13 final size:13
Alignment explanation
Indices: 9496--9521 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9486 CAATTTTTTG
9496 TGTATCGATACAT
1 TGTATCGATACAT
9509 TGTATCGATACAT
1 TGTATCGATACAT
9522 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9536 original size:32 final size:33
Alignment explanation
Indices: 9476--9539 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
9466 TACAAGCCAA
** *
9476 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
9509 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
9540 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:11947 original size:13 final size:13
Alignment explanation
Indices: 11929--11953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11919 CATTTTATGG
11929 TGTATCGATACAA
1 TGTATCGATACAA
11942 TGTATCGATACA
1 TGTATCGATACA
11954 TACTGTCTGT
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:12052 original size:20 final size:20
Alignment explanation
Indices: 12007--12060 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
11997 CAATGACCTA
**
12007 TATCGATACATCTTTTTCAAG
1 TATCGATACAT-TTGGTCAAG
*
12028 TATCGATACATTTGGTCATG
1 TATCGATACATTTGGTCAAG
12048 TATCGATACATTT
1 TATCGATACATTT
12061 AAATGTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (20 bp):
TATCGATACATTTGGTCAAG
Found at i:14495 original size:13 final size:13
Alignment explanation
Indices: 14477--14515 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
14467 ATAATCCCCT
14477 TGTATCGATACAG
1 TGTATCGATACAG
*
14490 TGTATCGATACAA
1 TGTATCGATACAG
14503 TGTATCGATACAG
1 TGTATCGATACAG
14516 AGAATGCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:17028 original size:59 final size:59
Alignment explanation
Indices: 16959--17078 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
16949 CATAGCTCGG
16959 TTTAAAACATAACAAGCGGTATTGATAGCCTTTGCCCAAAAATATCTTGGTAAATTATT
1 TTTAAAACATAACAAGCGGTATTGATAGCCTTTGCCCAAAAATATCTTGGTAAATTATT
17018 TTTAAAACATAACAAGCGGTATTGATAGCCTTTGCCCAAAAATATCTTGGTAAATTATT
1 TTTAAAACATAACAAGCGGTATTGATAGCCTTTGCCCAAAAATATCTTGGTAAATTATT
17077 TT
1 TT
17079 CACAAAGCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (59 bp):
TTTAAAACATAACAAGCGGTATTGATAGCCTTTGCCCAAAAATATCTTGGTAAATTATT
Found at i:18859 original size:19 final size:19
Alignment explanation
Indices: 18822--18859 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
18812 TCTTCAAGAG
18822 TTTTGAAGATTCATCGAAGC
1 TTTTGAAGATT-ATCGAAGC
18842 TTTTGAAGAATT-TCGAAG
1 TTTTGAAG-ATTATCGAAG
18860 AGTAGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
TTTTGAAGATTATCGAAGC
Found at i:20415 original size:13 final size:13
Alignment explanation
Indices: 20397--20421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20387 CATTTTATGG
20397 TGTATCGATACAA
1 TGTATCGATACAA
20410 TGTATCGATACA
1 TGTATCGATACA
20422 TACTGTGTGT
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:22548 original size:13 final size:13
Alignment explanation
Indices: 22530--22564 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
22520 AAGGATCTTA
22530 GTATCGATACATT
1 GTATCGATACATT
22543 GTATCGATACATT
1 GTATCGATACATT
22556 GTATCGATA
1 GTATCGATA
22565 TAAGGGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:24443 original size:21 final size:23
Alignment explanation
Indices: 24428--24471 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
24418 AAAAAGGGAA
24428 AGATTGTTTTATAAAAGAGATAG
1 AGATTGTTTTATAAAAGAGATAG
* *
24451 AGTTTGTTTTATAAAAAAGAT
1 AGATTGTTTTATAAAAGAGAT
24472 TATTTTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (23 bp):
AGATTGTTTTATAAAAGAGATAG
Found at i:26409 original size:24 final size:25
Alignment explanation
Indices: 26357--26409 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
26347 TGCTCTTTTG
* *
26357 TTTTTTTTTTTGTTTTGTTGTTGTC
1 TTTTTTTTTTTATTTTGTTCTTGTC
*
26382 TTTTTTTTTTCATTTT-TTCTT-TC
1 TTTTTTTTTTTATTTTGTTCTTGTC
26405 TTTTT
1 TTTTT
26410 CTTATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 4 0.16
25 14 0.56
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.83
Consensus pattern (25 bp):
TTTTTTTTTTTATTTTGTTCTTGTC
Found at i:28041 original size:13 final size:13
Alignment explanation
Indices: 28023--28049 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28013 ACAATTTTTT
28023 TTGTATCGATACA
1 TTGTATCGATACA
28036 TTGTATCGATACA
1 TTGTATCGATACA
28049 T
1 T
28050 ACTTGGTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:28133 original size:20 final size:21
Alignment explanation
Indices: 28088--28140 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
28078 CTGCCAAGAA
* **
28088 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTGTAAC
28109 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTGTAAC
28129 ATGTATCGATAC
1 ATGTATCGATAC
28141 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTGTAAC
Found at i:28816 original size:36 final size:36
Alignment explanation
Indices: 28775--28847 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
28765 TTGTTAATAA
28775 TTCTCCCCCTTAATCAAGTAATTCATATCAAAAATT
1 TTCTCCCCCTTAATCAAGTAATTCATATCAAAAATT
28811 TTCTCCCCCTTAATCAAGTAATTCATATCAAAAATT
1 TTCTCCCCCTTAATCAAGTAATTCATATCAAAAATT
28847 T
1 T
28848 ATTTGCACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (36 bp):
TTCTCCCCCTTAATCAAGTAATTCATATCAAAAATT
Found at i:30655 original size:13 final size:13
Alignment explanation
Indices: 30637--30662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30627 ATAATCACCC
30637 TGTATCGATACAA
1 TGTATCGATACAA
30650 TGTATCGATACAA
1 TGTATCGATACAA
30663 GGAAAAATGT
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):
TGTATCGATACAA
Found at i:32761 original size:15 final size:15
Alignment explanation
Indices: 32741--32771 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32731 ATTTCGTTTG
*
32741 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
32756 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
32771 G
1 G
32772 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:34597 original size:21 final size:22
Alignment explanation
Indices: 34572--34618 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
34562 GCAAGTTTTC
*
34572 ATTTTTCTTAGCTAAC-TCATT
1 ATTTTTATTAGCTAACTTCATT
*
34593 ATTTTTATTAGCTAACTTCTTT
1 ATTTTTATTAGCTAACTTCATT
34615 ATTT
1 ATTT
34619 CATCTTGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTTTTATTAGCTAACTTCATT
Found at i:36792 original size:20 final size:20
Alignment explanation
Indices: 36750--36788 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
36740 CGTGTAAATG
* *
36750 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
36770 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
36789 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:36857 original size:13 final size:13
Alignment explanation
Indices: 36839--36864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36829 CAATTTTTTG
36839 TGTATCGATACAT
1 TGTATCGATACAT
36852 TGTATCGATACAT
1 TGTATCGATACAT
36865 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36879 original size:32 final size:33
Alignment explanation
Indices: 36819--36882 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
36809 TACAAGCCAA
** *
36819 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
36852 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
36883 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:40129 original size:2 final size:2
Alignment explanation
Indices: 40122--40149 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40112 TATTCAAGAA
40122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40150 TGGTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41735 original size:32 final size:30
Alignment explanation
Indices: 41699--41757 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
41689 GAAATCAAAT
41699 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
41731 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
41758 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:42057 original size:13 final size:13
Alignment explanation
Indices: 42039--42064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42029 CAATTTTTTG
42039 TGTATCGATACAT
1 TGTATCGATACAT
42052 TGTATCGATACAT
1 TGTATCGATACAT
42065 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:42075 original size:32 final size:33
Alignment explanation
Indices: 42019--42082 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
42009 TACAAGCCAA
*
42019 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
42052 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
42083 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:42076 original size:19 final size:19
Alignment explanation
Indices: 42019--42082 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
42009 TACAAGCCAA
*
42019 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
42039 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
42052 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
42071 TGTATCGATACA
1 TGTATCGATACA
42083 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:42187 original size:20 final size:20
Alignment explanation
Indices: 42134--42189 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
42124 ACATCTTTTT
*
42134 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
42154 CATGTATGGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
42173 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
42190 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:43302 original size:15 final size:15
Alignment explanation
Indices: 43282--43310 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43272 AAGGTTCAGT
43282 TGACAAGTCAACGCA
1 TGACAAGTCAACGCA
43297 TGACAAGTCAACGC
1 TGACAAGTCAACGC
43311 GGCTAGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (15 bp):
TGACAAGTCAACGCA
Found at i:44580 original size:13 final size:13
Alignment explanation
Indices: 44562--44587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44552 TATAATCCCC
44562 TGTATCGATACAA
1 TGTATCGATACAA
44575 TGTATCGATACAA
1 TGTATCGATACAA
44588 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:46672 original size:15 final size:15
Alignment explanation
Indices: 46652--46682 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46642 ATTTCGTTTG
*
46652 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
46667 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
46682 G
1 G
46683 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:48484 original size:21 final size:21
Alignment explanation
Indices: 48455--48499 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
48445 AAGTTTTTAT
*
48455 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
48475 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
48497 TTT
1 TTT
48500 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:50767 original size:32 final size:33
Alignment explanation
Indices: 50709--50772 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
50699 TACAAGCCAA
*
50709 TGTATCGATACAATTTTTTGTATATCGATACAT
1 TGTATCGATACAATATTTTGTATATCGATACAT
*
50742 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTATATCGATACA
50773 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTATATCGATACAT
Found at i:50877 original size:20 final size:20
Alignment explanation
Indices: 50824--50879 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
50814 ACATCTTTTT
*
50824 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
50844 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
50863 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
50880 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:51416 original size:11 final size:12
Alignment explanation
Indices: 51392--51421 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
51382 TTTTGCAAGT
51392 AAAGAAAGAAAA
1 AAAGAAAGAAAA
51404 AAAGAAA-AAAA
1 AAAGAAAGAAAA
51415 AAAGAAA
1 AAAGAAA
51422 TAAAGGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:52584 original size:143 final size:141
Alignment explanation
Indices: 52315--53082 Score: 783
Period size: 143 Copynumber: 5.4 Consensus size: 141
52305 ATTTTATCAC
* * * * * *
52315 TAAATAAAAATCATTTTTTTAATTTTTCAAGATTTCTAATATT-TTCATGGGTATCTGTAGGTGT
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCT-ATATTCCT-AT-GGTTTCTGTAGGGGT
* * * * *
52379 ATAGAAAT-TTTAAAAACGTTACATATCTTTTCGGTTCTCCATTTAGGTATGAAATAAATTTTTT
63 ACAGAAATCTTT-AAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAAT-AATTTTTT
*
52443 TTGGAAATTAAAAAGT
126 TTGGAAATTAAAAAAT
* * * * *
52459 TAAATAAAAACTATCATTTTAATTTTTCAAGATTTCTATATTTCTATTGTTTCTGTAGGGGTTAC
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTCTGTAGGGG-TAC
* * * ** *
52524 AAAAATCTTTAAAACTTTTTATATTTTTTCAATTCTCCATTAAGGTACGAAATAATTTTTTTTTT
65 AGAAATCTTTAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATAA-TTTTTTTTG
*
52589 TAAATTAAAAAAT
129 GAAATTAAAAAAT
* * * *
52602 TAAATACAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTTTCATAGGTGTTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTCT-GTAGG-GGTA
* * * * * *
52667 CAGAAATCTTCAAAACTTTTCGTATCTTTTCAGTTCTCTATTAAGGTATGAAATGATTTTTTTT-
64 CAGAAATCTTTAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATAATTTTTTTTG
* *
52731 TAAATTAAAAGAT
129 GAAATTAAAAAAT
* * * *
52744 TAAATAAAAATTATTATCTTAATATTT-ATAGATTTCTATATTCCTATAGTTTTCTGTAAGGGTG
1 TAAATAAAAATTATTATCTTAATTTTTCA-AGATTTCTATATTCCTAT-GGTTTCTGTAGGGGTA
* * ** * * *
52808 CAGAAATCTTCAAAACTTTTCGTATCTTTTCGACTCTTCATTAAGGTACAAAATAAATTTTTTTG
64 CAGAAATCTTTAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATAATTTTTTTTG
*
52873 GAAAATAAAAAAT
129 GAAATTAAAAAAT
* * * * * *
52886 TAAATAAAAATTATTATCTTAATTTTTCTAGATTTTTATATTCCTATGGTTTTTCGTTGTGGTAT
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTCT-GTAGGGGTAC
* * * *
52951 AGAAATCTTTAAAACTTTTCATATTTTTTTTTGGTTCTCTATTAAAGTACGAAATGAA--TTTTT
65 AGAAATCTTTAAAACTTTTCATA--TCTTTTCGGTTCTCCATTAAGGTACGAAAT-AATTTTTTT
*
53014 TGAAAATTAAAAAAT
127 TGGAAATTAAAAAAT
* * *
53029 TAAATAAAAATTATCATCATAATTTTTTAAGATTTTCTAATATTCCTATGGTTT
1 TAAATAAAAATTATTATCTTAATTTTTCAAGA-TTTCT-ATATTCCTATGGTTT
53083 TCCATAGGGA
Statistics
Matches: 521, Mismatches: 87, Indels: 31
0.82 0.14 0.05
Matches are distributed among these distances:
141 63 0.12
142 150 0.29
143 174 0.33
144 116 0.22
145 18 0.03
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (141 bp):
TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTCTGTAGGGGTACA
GAAATCTTTAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATAATTTTTTTTGGA
AATTAAAAAAT
Found at i:52787 original size:142 final size:141
Alignment explanation
Indices: 52402--53120 Score: 715
Period size: 142 Copynumber: 5.0 Consensus size: 141
52392 AAACGTTACA
* * * * *
52402 TATCTTTTCGGTTCTCCATTTAGGTATGAAATAAATTTTTTTTGGAAATTAAAAAGTTAAATAAA
1 TATCTTTTCAGTTCTCTATTAAGGTACGAAAT-AATTTTTTTT-GAAATTAAAAAATTAAATAAA
* * * * * * *
52467 AACTATCATTTTAATTTTTCA-AGATTTCTATATTTCTATTGTTTCT-GTAGGGGTTACAAAAAT
64 AATTATTATCTTAATTTTT-ATAGATTTCTATATTCCTATGGTTTTTCGTA-GGGTTACAGAAAT
* **
52530 CTTTAAAACTTTTTA
127 CTTCAAAACTTTTCG
* * * * *
52545 TATTTTTTCAATTCTCCATTAAGGTACGAAATAATTTTTTTTTTTAAATTAAAAAATTAAATACA
1 TATCTTTTCAGTTCTCTATTAAGGTACGAAATAA--TTTTTTTTGAAATTAAAAAATTAAATAAA
*
52610 AATTATTATCTTAATTTTTCA-AGATTTCTATATTCCTATGGTTTTTCATAGGTGTTACAGAAAT
64 AATTATTATCTTAATTTTT-ATAGATTTCTATATTCCTATGGTTTTTCGTAGG-GTTACAGAAAT
52674 CTTCAAAACTTTTCG
127 CTTCAAAACTTTTCG
* * * *
52689 TATCTTTTCAGTTCTCTATTAAGGTATGAAATGATTTTTTTTTAAATTAAAAGATTAAATAAAAA
1 TATCTTTTCAGTTCTCTATTAAGGTACGAAATAATTTTTTTTGAAATTAAAAAATTAAATAAAAA
* * *
52754 TTATTATCTTAATATTTATAGATTTCTATATTCCTATAG-TTTTCTGTAAGGG-TGCAGAAATCT
66 TTATTATCTTAATTTTTATAGATTTCTATATTCCTATGGTTTTTC-GT-AGGGTTACAGAAATCT
52817 TCAAAACTTTTCG
129 TCAAAACTTTTCG
* * * *
52830 TATCTTTTC-G-ACTCTTCATTAAGGTACAAAATAAATTTTTTTGGAAAATAAAAAATTAAATAA
1 TATCTTTTCAGTTCTC-T-ATTAAGGTACGAAAT-AATTTTTTTTGAAATTAAAAAATTAAATAA
* * * *
52893 AAATTATTATCTTAATTTTTCTAGATTTTTATATTCCTATGGTTTTTCGTTGTGG-TATAGAAAT
63 AAATTATTATCTTAATTTTTATAGATTTCTATATTCCTATGGTTTTTCGTAG-GGTTACAGAAAT
* *
52957 CTTTAAAACTTTTCA
127 CTTCAAAACTTTTCG
* ** *
52972 TATTTTTTTTTGGTTCTCTATTAAAGTACGAAATGAA--TTTTTTGAAAATTAAAAAATTAAATA
1 TA--TCTTTTCAGTTCTCTATTAAGGTACGAAAT-AATTTTTTTTG-AAATTAAAAAATTAAATA
* * * * * * *
53035 AAAATTATCATCATAATTTTT-TAAGATTTTCTAATATTCCTATGGTTTTCCATAGGGATATAAA
62 AAAATTATTATCTTAATTTTTAT-AGA-TTTCT-ATATTCCTATGGTTTTTCGTAGGGTTACAGA
*
53099 AATTTTCAAAAC-TTTCG
124 AATCTTCAAAACTTTTCG
53116 TATCT
1 TATCT
53121 CCTAGTTTTT
Statistics
Matches: 489, Mismatches: 66, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
139 3 0.01
140 2 0.00
141 52 0.11
142 166 0.34
143 134 0.27
144 93 0.19
145 36 0.07
146 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (141 bp):
TATCTTTTCAGTTCTCTATTAAGGTACGAAATAATTTTTTTTGAAATTAAAAAATTAAATAAAAA
TTATTATCTTAATTTTTATAGATTTCTATATTCCTATGGTTTTTCGTAGGGTTACAGAAATCTTC
AAAACTTTTCG
Found at i:52852 original size:285 final size:282
Alignment explanation
Indices: 52315--53113 Score: 856
Period size: 285 Copynumber: 2.8 Consensus size: 282
52305 ATTTTATCAC
* * * * * *
52315 TAAATAAAAATCATTTTTTTAATTTTTCAAGATTTCTAATATT-TTCATGG-GTATCTGTAGGTG
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCT-ATATTCCT-ATGGTTTTTC-GTAGGTG
* * * * * *
52378 TATAGAAATTTTAAAAACGTTACATATCTTTTCGGTTCTCCATTTAGGTATGAAATAAATTTTTT
63 TATAGAAATCTTAAAAACTTTTCATATCTTTTCGGTTCTCTATTAAGGTATGAAAT-GATTTTTT
* * * * *
52443 TTGGAAATTAAAAAGTTAAATAAAAACTATCATTTTAATTTT-TCAAGATTTCTATATTTCTATT
127 TT-AAAATTAAAAA-TTAAATAAAAATTATCATCTTAATTTTAT--AGATTTCTATATTCCTATA
* * * * *
52507 G-TTTCTGTAGGGGTTACAAAAATCTTTAAAACTTTTTATATTTTTTCAATTCTCCATTAAGGTA
188 GTTTTCTGTAAGGGTTACAAAAATCTTCAAAACTTTTCATATCTTTTCAACTCTCCATTAAGGTA
* * ** *
52571 CGAAATAATTTTTTTTTTTAAATTAAAAAAT
253 CAAAATAA-ATTTTTTTGGAAAATAAAAAAT
* *
52602 TAAATACAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTTTCATAGGTGTTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTTTCGTAGGTG-TA
* * * * *
52667 CAGAAATCTTCAAAACTTTTCGTATCTTTTCAGTTCTCTATTAAGGTATGAAATGATTTTTTTTT
65 TAGAAATCTTAAAAACTTTTCATATCTTTTCGGTTCTCTATTAAGGTATGAAATGATTTTTTTTA
*
52732 AAATTAAAAGATTAAATAAAAATTATTATCTTAATATTTATAGATTTCTATATTCCTATAGTTTT
130 AAATTAAAA-ATTAAATAAAAATTATCATCTTAAT-TTTATAGATTTCTATATTCCTATAGTTTT
* * * * *
52797 CTGTAAGGG-TGCAGAAATCTTCAAAACTTTTCGTATCTTTTCGACTCTTCATTAAGGTACAAAA
193 CTGTAAGGGTTACAAAAATCTTCAAAACTTTTCATATCTTTTCAACTCTCCATTAAGGTACAAAA
52861 TAAATTTTTTTGGAAAATAAAAAAT
258 TAAATTTTTTTGGAAAATAAAAAAT
* * *
52886 TAAATAAAAATTATTATCTTAATTTTTCTAGATTTTTATATTCCTATGGTTTTTCGT-TGTGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTTTCGTAGGT-GTA
* * * * * *
52950 TAGAAATCTTTAAAACTTTTCATATTTTTTTTTGGTTCTCTATTAAAGTACGAAATGAATTTTTT
65 TAGAAATCTTAAAAACTTTTCATA--TCTTTTCGGTTCTCTATTAAGGTATGAAATGATTTTTTT
* * * *
53015 GAAAATTAAAAAATTAAATAAAAATTATCATCATAATTTTTTAAGATTTTCTAATATTCCTATGG
128 TAAAATT-AAAAATTAAATAAAAATTATCATCTTAATTTTAT-AGA-TTTCT-ATATTCCTATAG
** * * *
53080 TTTTCCAT-AGGGATATAAAAATTTTCAAAACTTT
189 TTTTCTGTAAGGGTTACAAAAATCTTCAAAACTTT
53114 CGTATCTCCT
Statistics
Matches: 432, Mismatches: 65, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
283 25 0.06
284 76 0.18
285 160 0.37
286 52 0.12
287 119 0.28
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (282 bp):
TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATATTCCTATGGTTTTTCGTAGGTGTAT
AGAAATCTTAAAAACTTTTCATATCTTTTCGGTTCTCTATTAAGGTATGAAATGATTTTTTTTAA
AATTAAAAATTAAATAAAAATTATCATCTTAATTTTATAGATTTCTATATTCCTATAGTTTTCTG
TAAGGGTTACAAAAATCTTCAAAACTTTTCATATCTTTTCAACTCTCCATTAAGGTACAAAATAA
ATTTTTTTGGAAAATAAAAAAT
Found at i:56732 original size:29 final size:29
Alignment explanation
Indices: 56684--56857 Score: 199
Period size: 29 Copynumber: 6.0 Consensus size: 29
56674 AGGGAAATTC
* *
56684 TAGTGTTTTACTTGAATTTTAATTCCTTT
1 TAGTGTTTTAGTTGACTTTTAATTCCTTT
*
56713 TAGTGTTTTAGTTTACTTTTAATTCCTTT
1 TAGTGTTTTAGTTGACTTTTAATTCCTTT
* *
56742 TTGTGTTTTAGTTGACTTTTAATT-ATATT
1 TAGTGTTTTAGTTGACTTTTAATTCCT-TT
* * *
56771 TTGTGTTTTAGTTGACTTTTTATTCTTTT
1 TAGTGTTTTAGTTGACTTTTAATTCCTTT
* *
56800 TAGTGGTTTAGTTGACCTTTAATTCCTTTT
1 TAGTGTTTTAGTTGACTTTTAATTCC-TTT
* *
56830 TA-TGTTTTAATTGACTTTTTGATTCCTT
1 TAGTGTTTTAGTTGAC-TTTTAATTCCTT
56858 AGCTTTATAT
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
28 1 0.01
29 109 0.88
30 14 0.11
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (29 bp):
TAGTGTTTTAGTTGACTTTTAATTCCTTT
Found at i:56836 original size:87 final size:87
Alignment explanation
Indices: 56686--56848 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
56676 GGAAATTCTA
* * * *
56686 GTGTTTTACTTGAATTTTAATTCCTTTTAGTGTTTTAGTTTACTTTTAATTCCTTTTTGTGTTTT
1 GTGTTTTACTTGAATTTTAATTCCTTTTAGTGGTTTAGTTGACCTTTAATTCCTTTTTATGTTTT
*
56751 AGTTGACTTTTAATTATATTTT
66 AATTGACTTTTAATTATATTTT
* * * *
56773 GTGTTTTAGTTGACTTTTTATTCTTTTTAGTGGTTTAGTTGACCTTTAATTCCTTTTTATGTTTT
1 GTGTTTTACTTGAATTTTAATTCCTTTTAGTGGTTTAGTTGACCTTTAATTCCTTTTTATGTTTT
56838 AATTGACTTTT
66 AATTGACTTTT
56849 TGATTCCTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (87 bp):
GTGTTTTACTTGAATTTTAATTCCTTTTAGTGGTTTAGTTGACCTTTAATTCCTTTTTATGTTTT
AATTGACTTTTAATTATATTTT
Found at i:57595 original size:25 final size:25
Alignment explanation
Indices: 57561--57608 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
57551 TTCTAAAAAT
*
57561 CGAGTTTTAGAACT-TTTCATCTAAA
1 CGAGTCTTAGAACTATTT-ATCTAAA
*
57586 CGAGTCTTAGGACTATTTATCTA
1 CGAGTCTTAGAACTATTTATCTA
57609 TTAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (25 bp):
CGAGTCTTAGAACTATTTATCTAAA
Found at i:59377 original size:13 final size:13
Alignment explanation
Indices: 59359--59416 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
59349 AATTTGGTCA
59359 TGTATCGATACAT
1 TGTATCGATACAT
59372 TGTATCGATACATCTTGT
1 TGTATCGATACA-----T
59390 ATGTATCGATACAT
1 -TGTATCGATACAT
59404 TGTATCGATACAT
1 TGTATCGATACAT
59417 CTTGTATGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 25 0.64
14 1 0.03
18 1 0.03
19 12 0.31
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:59396 original size:19 final size:19
Alignment explanation
Indices: 59372--59434 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
59362 ATCGATACAT
59372 TGTATCGATACATCTTGTA
1 TGTATCGATACATCTTGTA
59391 TGTATCGATACA-----T-
1 TGTATCGATACATCTTGTA
59404 TGTATCGATACATCTTGTA
1 TGTATCGATACATCTTGTA
59423 TGTATCGATACA
1 TGTATCGATACA
59435 AATAGTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
18 1 0.03
19 24 0.63
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATCTTGTA
Found at i:59399 original size:32 final size:32
Alignment explanation
Indices: 59338--59434 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
59328 TACAAGCCAA
59338 TGTATCGATACAAT-TTGGTCATGTATCGATACAT
1 TGTATCGATAC-ATCTT-GT-ATGTATCGATACAT
59372 TGTATCGATACATCTTGTATGTATCGATACAT
1 TGTATCGATACATCTTGTATGTATCGATACAT
59404 TGTATCGATACATCTTGTATGTATCGATACA
1 TGTATCGATACATCTTGTATGTATCGATACA
59435 AATAGTTAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
32 45 0.73
33 4 0.06
34 13 0.21
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGTATGTATCGATACAT
Found at i:61532 original size:20 final size:22
Alignment explanation
Indices: 61493--61536 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
61483 GCTGTGAATG
*
61493 TGGGGGTTGCCCGGTTGCGACC
1 TGGGGGTTGCCCGGTCGCGACC
61515 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGTTGCCCGGTCGCGACC
61535 TG
1 TG
61537 ATGAGTGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.05, C:0.27, G:0.48, T:0.20
Consensus pattern (22 bp):
TGGGGGTTGCCCGGTCGCGACC
Found at i:67326 original size:15 final size:13
Alignment explanation
Indices: 67294--67319 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67284 AATTTGGTCA
67294 TGTATCGATACAT
1 TGTATCGATACAT
67307 TGTATCGATACAT
1 TGTATCGATACAT
67320 CTTGTATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:67430 original size:20 final size:21
Alignment explanation
Indices: 67379--67433 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
67369 GCCAATCACC
*
67379 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
* *
67400 AGTATCAATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
67420 TGTATCGATACATT
1 TGTATCGATACATT
67434 GTATCGATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.04
20 15 0.54
21 12 0.43
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:69946 original size:2 final size:2
Alignment explanation
Indices: 69941--69969 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
69931 TCTCTCATGC
69941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69970 AAAAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73459 original size:2 final size:2
Alignment explanation
Indices: 73452--73482 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73442 CAACCGAGTT
73452 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 T
73483 GACTAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74551 original size:18 final size:19
Alignment explanation
Indices: 74513--74557 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
74503 ATTATGTCTT
*
74513 ATTGATTTTTTATTTTGTG
1 ATTGATTTTTTATTCTGTG
74532 ATTAGATTTTTT-TTCT-TG
1 ATT-GATTTTTTATTCTGTG
74550 ATTGATTT
1 ATTGATTT
74558 CAATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 5 0.21
19 6 0.25
20 8 0.33
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (19 bp):
ATTGATTTTTTATTCTGTG
Found at i:76341 original size:78 final size:77
Alignment explanation
Indices: 76210--76396 Score: 223
Period size: 77 Copynumber: 2.4 Consensus size: 77
76200 TCTCACATAA
* * *
76210 CTTAATGGACATGTATCGACACG-AGGTTCCCACATGATCTTAAGGACTCAATTTTAAGATAATA
1 CTTAATGGACATGTTTCAACACGAAGGTTCCCACATGATCTTAAAGACTCAATTTTAAGATAATA
*
76274 TTACTTAAATAC
66 TTACGTAAATAC
* * * * * * * *
76286 TTTTAATGGACATGTTTCAACATGAAAGTTCCTACGTGATCTTAAAGACTTAATTTTAAGGTAGT
1 -CTTAATGGACATGTTTCAACACGAAGGTTCCCACATGATCTTAAAGACTCAATTTTAAGATAAT
76351 ATTACGTAAATAC
65 ATTACGTAAATAC
* * *
76364 CTTAATGAACATCTTTTAACACGAAGGTTCCCA
1 CTTAATGGACATGTTTCAACACGAAGGTTCCCA
76397 TATAATCCTA
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
77 45 0.50
78 45 0.50
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (77 bp):
CTTAATGGACATGTTTCAACACGAAGGTTCCCACATGATCTTAAAGACTCAATTTTAAGATAATA
TTACGTAAATAC
Found at i:76664 original size:58 final size:57
Alignment explanation
Indices: 76493--76682 Score: 145
Period size: 58 Copynumber: 3.3 Consensus size: 57
76483 AAAGTGACTT
* * * *
76493 TAAAATACATAAAATTATATAA-AAGTCCTTAAAACATGAAAAAATGCCTAAAATGAGCC
1 TAAAATGCATAAAATTATATAATAA-TCCTTAAATCATG--AAAATGACTAAAATGAACC
* * * * * **
76552 TATAATGCATGAAATTGCATA-AATGAT-CTTAAATCATGGCAAATTACTGGAATGAACC
1 TAAAATGCATAAAATT--ATATAATAATCCTTAAATCAT-GAAAATGACTAAAATGAACC
* * *
76610 TAAAATGCATAAAATTATATAATAATCCCTAATTCATGAATAATGACTAAAATG-ACA
1 TAAAATGCATAAAATTATATAATAATCCTTAAATCATGAA-AATGACTAAAATGAACC
*
76667 TAAAAATGCATGAAAT
1 T-AAAATGCATAAAAT
76683 AACATAAAAG
Statistics
Matches: 101, Mismatches: 22, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
56 3 0.03
57 10 0.10
58 58 0.57
59 22 0.22
60 4 0.04
61 4 0.04
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (57 bp):
TAAAATGCATAAAATTATATAATAATCCTTAAATCATGAAAATGACTAAAATGAACC
Found at i:77548 original size:17 final size:17
Alignment explanation
Indices: 77526--77568 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
77516 GCTCACATAG
77526 AAATGAAAGAATATGTA
1 AAATGAAAGAATATGTA
77543 AAATGAAAGAATATGTA
1 AAATGAAAGAATATGTA
77560 AAATGAAAG
1 AAATGAAAG
77569 TAAAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (17 bp):
AAATGAAAGAATATGTA
Found at i:77646 original size:18 final size:19
Alignment explanation
Indices: 77623--77671 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
77613 AAACCCTATT
77623 TTTTTTTCTTTTTCTTT-C
1 TTTTTTTCTTTTTCTTTCC
*
77641 TTTTTTTCTTTTTTTTTTCC
1 TTTTTTTC-TTTTTCTTTCC
77661 TTTTTTT-TTTT
1 TTTTTTTCTTTT
77672 AAGTTTCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.43
19 8 0.29
20 8 0.29
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (19 bp):
TTTTTTTCTTTTTCTTTCC
Found at i:77648 original size:12 final size:11
Alignment explanation
Indices: 77621--77670 Score: 66
Period size: 12 Copynumber: 4.5 Consensus size: 11
77611 AAAAACCCTA
*
77621 TTTTT-TTTTC
1 TTTTTCTTTTT
77631 TTTTTCTTTCTT
1 TTTTTCTTT-TT
77643 TTTTTCTTTTT
1 TTTTTCTTTTT
77654 TTTTTCCTTTTT
1 TTTTT-CTTTTT
77666 TTTTT
1 TTTTT
77671 TAAGTTTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 5 0.14
11 10 0.28
12 21 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:79291 original size:2 final size:2
Alignment explanation
Indices: 79284--79314 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
79274 AAAAGATAAT
79284 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
79315 ACAAGTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:82598 original size:2 final size:2
Alignment explanation
Indices: 82591--82634 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
82581 ACATACATAC
82591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82633 TA
1 TA
82635 ACCTCCGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83332 original size:14 final size:14
Alignment explanation
Indices: 83313--83339 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
83303 CTAACTACGA
83313 GAAAAAAGAAAAAG
1 GAAAAAAGAAAAAG
83327 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
83340 AATCAAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
GAAAAAAGAAAAAG
Found at i:87703 original size:13 final size:13
Alignment explanation
Indices: 87666--87712 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
87656 AAATAATAAT
*
87666 ATATTTTATCATA
1 ATATTTTATTATA
*
87679 ATAATTTA-TATA
1 ATATTTTATTATA
*
87691 TTATTTTATTATA
1 ATATTTTATTATA
*
87704 ATAATTTAT
1 ATATTTTAT
87713 ACATTGTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTTTATTATA
Found at i:89434 original size:2 final size:2
Alignment explanation
Indices: 89423--89462 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
89413 AATAGAAAGA
89423 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89463 AATAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91176 original size:13 final size:13
Alignment explanation
Indices: 91158--91182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
91148 CAATTCATCA
91158 TGTATCGATACAT
1 TGTATCGATACAT
91171 TGTATCGATACA
1 TGTATCGATACA
91183 ATGTGCTATG
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:91180 original size:33 final size:33
Alignment explanation
Indices: 91138--91202 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
91128 TTTGAAGCAA
91138 TGTATCGATACAAT-T-CATCATGTATCGATACAT
1 TGTATCGATACAATGTGC-T-ATGTATCGATACAT
91171 TGTATCGATACAATGTGCTATGTATCGATACA
1 TGTATCGATACAATGTGCTATGTATCGATACA
91203 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.90
34 2 0.07
35 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTGCTATGTATCGATACAT
Found at i:91329 original size:20 final size:20
Alignment explanation
Indices: 91306--91358 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
91296 CAAAGCATAA
* *
91306 TGTATTGATATATCTGGGTG
1 TGTATCGATACATCTGGGTG
91326 TGTATCGATACATCTGGGTG
1 TGTATCGATACATCTGGGTG
91346 TGTATCGATACAT
1 TGTATCGATACAT
91359 ATAAGGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATCTGGGTG
Found at i:93841 original size:13 final size:13
Alignment explanation
Indices: 93823--93885 Score: 108
Period size: 13 Copynumber: 4.8 Consensus size: 13
93813 GTAACCCATA
*
93823 TATCGATATAATG
1 TATCGATACAATG
93836 TATCGATACAATG
1 TATCGATACAATG
*
93849 TATCGATATAATG
1 TATCGATACAATG
93862 TATCGATACAATG
1 TATCGATACAATG
93875 TATCGATACAA
1 TATCGATACAA
93886 AAAATATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:93852 original size:26 final size:26
Alignment explanation
Indices: 93823--93882 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
93813 GTAACCCATA
93823 TATCGATATAATGTATCGATACAATG
1 TATCGATATAATGTATCGATACAATG
93849 TATCGATATAATGTATCGATACAATG
1 TATCGATATAATGTATCGATACAATG
93875 TATCGATA
1 TATCGATA
93883 CAAAAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (26 bp):
TATCGATATAATGTATCGATACAATG
Found at i:100479 original size:2 final size:2
Alignment explanation
Indices: 100472--100514 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
100462 ATCCTAACAG
*
100472 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100514 T
1 T
100515 TAAGGACAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:102978 original size:35 final size:36
Alignment explanation
Indices: 102911--102992 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
102901 TCCTTGAAGC
102911 AAATTTCAAGATCAAGCTTCAAAAAACCCTAGAAAT
1 AAATTTCAAGATCAAGCTTCAAAAAACCCTAGAAAT
* * **
102947 AAATTTTAAGATCAAG-TCTCAAAAAA-TCTAGAAGC
1 AAATTTCAAGATCAAGCT-TCAAAAAACCCTAGAAAT
102982 AAATTTCAAGA
1 AAATTTCAAGA
102993 ACAAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 17 0.43
36 23 0.57
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (36 bp):
AAATTTCAAGATCAAGCTTCAAAAAACCCTAGAAAT
Found at i:103040 original size:71 final size:71
Alignment explanation
Indices: 102875--103041 Score: 169
Period size: 71 Copynumber: 2.4 Consensus size: 71
102865 ACACTTGAAG
* *** * * **
102875 CAAATTTCAAGATCAATTCTC-AATGGTCCTTGAAGCAAATTTCAAGATCAAGCTTCAAAAAACC
1 CAAATTTCAAGATCAAGTCTCAAAAAAT-CTAGAAGCAAATTTCAAGAACAAAATTCAAAAAACC
102939 CTAGAAA
65 CTAGAAA
* * * *
102946 TAAATTTTAAGATCAAGTCTCAAAAAATCTAGAAGCAAATTTCAAGAACAAAATT-TAAAGACCC
1 CAAATTTCAAGATCAAGTCTCAAAAAATCTAGAAGCAAATTTCAAGAACAAAATTCAAAAAACCC
103010 TTA-AAA
66 -TAGAAA
*
103016 CAAATTTCCAGATCAAGTCATCAAAA
1 CAAATTTCAAGATCAAGTC-TCAAAA
103042 CCTTTGAAAC
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
70 26 0.33
71 49 0.63
72 3 0.04
ACGTcount: A:0.47, C:0.19, G:0.10, T:0.25
Consensus pattern (71 bp):
CAAATTTCAAGATCAAGTCTCAAAAAATCTAGAAGCAAATTTCAAGAACAAAATTCAAAAAACCC
TAGAAA
Found at i:104709 original size:22 final size:22
Alignment explanation
Indices: 104669--104710 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
104659 TCTTCGTACC
*
104669 TTCCTAGAGCACTGAGAGAACT
1 TTCCTAGAGCACCGAGAGAACT
*
104691 TTCCTAGAGCACCGGGAGAA
1 TTCCTAGAGCACCGAGAGAA
104711 TGCAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (22 bp):
TTCCTAGAGCACCGAGAGAACT
Found at i:105584 original size:155 final size:151
Alignment explanation
Indices: 105404--105913 Score: 510
Period size: 155 Copynumber: 3.3 Consensus size: 151
105394 TTATAGATAA
* * *
105404 GATGAACCTATCCTAAATACCCACCTTCGACATAAAAGTGGACCCAGTGACAACCTAAGAGTTGG
1 GATGAACCTATCCTAAATATCCACCTTCGACATAAAAGTGGACCCAGTGACGACCTAGGAGTTGG
*
105469 TTTTGAAAAATTACAAAGATACTCCTAGAGGATACCTTCGACGTAGAAGTACTCGATACCCCTAA
66 TTTTG-AAAATTACAAA-ATAC-CCTAGGGGATACCTTCGACGTA-AAGTACTCGATACCCCTAA
105534 AGGATCTAAAAATGATTTT-AAAGG
127 AGGATCTAAAAATGATTTTAAAAGG
* * **
105558 AGATAAACCTATCTTAAATATCCACCTTCGACATAAAA-TCGGACCTGGTGACGACCTAGGAGTT
1 -GATGAACCTATCCTAAATATCCACCTTCGACATAAAAGT-GGACCCAGTGACGACCTAGGAGTT
* * ** *
105622 AGTTTTGGAAAATTACAAAAATACCCATAGGGGATATCTTCGACGTAAACGTACAGGATACCTCT
64 GGTTTT-GAAAATTAC-AAAATACCC-TAGGGGATACCTTCGACGTAAA-GTACTCGATACCCCT
*
105687 AAA-GAACTTAAAAA-GTATTTTAAAAGG
125 AAAGGATC-TAAAAATG-ATTTTAAAAGG
* * *** * *
105714 GATGAACTTATCCTAAATATCCACCATT-GGCATAAAAGTGGACCCAACAATGACCTAGGTGTTG
1 GATGAACCTATCCTAAATATCCACC-TTCGACATAAAAGTGGACCCAGTGACGACCTAGGAGTTG
* * * * * *
105778 GTTTTGGAAATTATGAAAATGCCTCTAGGGGATACCTTCGATGTAAAAGTA-TCTAATACTCCTA
65 GTTTTGAAAATTA-CAAAATACC-CTAGGGGATACCTTCGACGT-AAAGTACTC-GATACCCCTA
*
105842 AAGGACTCGAAAAATGATTTTAAAAGG
126 AAGGA-TCTAAAAATGATTTTAAAAGG
* * * * * *
105869 GATGAACCTATCATAGATATCTACCTTTGGCATAAAAGTAGACCC
1 GATGAACCTATCCTAAATATCCACCTTCGACATAAAAGTGGACCC
105914 GACGATGACA
Statistics
Matches: 294, Mismatches: 43, Indels: 36
0.79 0.12 0.10
Matches are distributed among these distances:
154 54 0.18
155 226 0.77
156 14 0.05
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (151 bp):
GATGAACCTATCCTAAATATCCACCTTCGACATAAAAGTGGACCCAGTGACGACCTAGGAGTTGG
TTTTGAAAATTACAAAATACCCTAGGGGATACCTTCGACGTAAAGTACTCGATACCCCTAAAGGA
TCTAAAAATGATTTTAAAAGG
Found at i:107342 original size:12 final size:12
Alignment explanation
Indices: 107327--107359 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
107317 TAGCTAGTTT
107327 TCTATTTTCTTC
1 TCTATTTTCTTC
107339 TCTATTTTC-TC
1 TCTATTTTCTTC
107350 TCT-TTTTCTT
1 TCTATTTTCTT
107360 TTGTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 6 0.30
12 9 0.45
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTATTTTCTTC
Found at i:108255 original size:166 final size:166
Alignment explanation
Indices: 107890--108268 Score: 369
Period size: 166 Copynumber: 2.3 Consensus size: 166
107880 TTTCAAAGAA
* * * ** * * *
107890 AAAAATT-CAAAACTCATAAAAATGAATTAATTTTTTAAAACTGATATAATATGAATCAAATAAT
1 AAAAATTGAAAAAGTCATAAAAATAAAAGAATTTTTTAAAACTGATTTAACAAGAATCAAATAAT
* *
107954 AATATTTGATAAATTTTAAAAATTGATAACCGAGAAAAATCCCCCGATAAAAATTTACATAGTAA
66 AATATTTGATAAATTTTAAAAATTGATAACCAAGAAAAATCCCCCGATAAAAATTTACAAAGTAA
* * * * *
108019 AAAACTCCGTATTATGAAAATAGGAGATTTTAAAGG
131 AAAACTCCGAATTATGAAAAAAGGAAATTCTAAAAG
* * *
108055 AAAAATTGAAAAATTTATAAAAATAAATGAATTTTTTAAAACTGATTTAACAAGAAAT-AAATAA
1 AAAAATTGAAAAAGTCATAAAAATAAAAGAATTTTTTAAAACTGATTTAACAAG-AATCAAATAA
* * * * *
108119 TAATATTTGATGAATTTTAAAAATT-TTGGATCAATG-AAAATCCTCCCGA-AAAAATTTATAAA
65 TAATATTTGATAAATTTTAAAAATTGAT-AACCAA-GAAAAATCC-CCCGATAAAAATTTACAAA
* * * *
108181 GTAGAAAACTTCGAATTTTTAAAACAAGAGAAATTCTAAAAG
127 GTAAAAAACTCCGAATTATGAAAA-AAG-GAAATTCTAAAAG
* * *
108223 -AAAATT-AAGAAGTCAT-AAAATAAAAAGAATTTTTCAAAATTGATTT
1 AAAAATTGAAAAAGTCATAAAAAT-AAAAGAATTTTTTAAAACTGATTT
108269 TATGGTGATT
Statistics
Matches: 176, Mismatches: 30, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
165 13 0.07
166 136 0.77
167 17 0.10
168 10 0.06
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.31
Consensus pattern (166 bp):
AAAAATTGAAAAAGTCATAAAAATAAAAGAATTTTTTAAAACTGATTTAACAAGAATCAAATAAT
AATATTTGATAAATTTTAAAAATTGATAACCAAGAAAAATCCCCCGATAAAAATTTACAAAGTAA
AAAACTCCGAATTATGAAAAAAGGAAATTCTAAAAG
Found at i:108486 original size:11 final size:11
Alignment explanation
Indices: 108470--108501 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
108460 TGAAATTATC
108470 AAATTTAAAAT
1 AAATTTAAAAT
*
108481 AAATTTGAAAT
1 AAATTTAAAAT
108492 AAATTTAAAA
1 AAATTTAAAA
108502 GAAGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:111888 original size:22 final size:20
Alignment explanation
Indices: 111839--111894 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
111829 AAAAACCCAG
*
111839 AATGTATCGATGCAATGAGC
1 AATGTATCGATACAATGAGC
111859 AATGTATCGATACAATTGTAAGC
1 AATGTATCGATACAA-TG--AGC
111882 -ATGTATCGATACA
1 AATGTATCGATACA
111895 TTTAGTAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 13 0.41
23 3 0.09
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:116519 original size:20 final size:21
Alignment explanation
Indices: 116494--116547 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
116484 CATTTTAGGC
116494 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
*
116514 ATGTATCGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
116535 TTGTATCGATACA
1 ATGTATCGATACA
116548 AATTATAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:117263 original size:20 final size:20
Alignment explanation
Indices: 117238--117307 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
117228 TTTACCCAGA
117238 TGTATCGATACATTTTACAT
1 TGTATCGATACATTTTACAT
117258 TGTATCGATACATTTCT-CAT
1 TGTATCGATACATTT-TACAT
*
117278 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTTACAT
117298 TGTATCGATA
1 TGTATCGATA
117308 TATTCAAGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTACAT
Found at i:117856 original size:38 final size:39
Alignment explanation
Indices: 117750--117856 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 39
117740 CAGCAGCAAG
117750 AAACCCTGAGGAAATCCTTTTATC-AA-CAAAAAAACCAA
1 AAACCCTGAGGAAATCCTTTTATCAAACCAAAAAAA-CAA
* ** ** * *
117788 AAACACAAAAAAAATACTATTTCATTAAACCAAAAAAA-AA
1 AAACCCTGAGGAAATCCT-TTT-ATCAAACCAAAAAAACAA
117828 AAACCCTGAGGAAATCCTTTTATCAAACC
1 AAACCCTGAGGAAATCCTTTTATCAAACC
117857 CTATTCCCGT
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
38 19 0.37
39 6 0.12
40 16 0.31
41 2 0.04
42 8 0.16
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.20
Consensus pattern (39 bp):
AAACCCTGAGGAAATCCTTTTATCAAACCAAAAAAACAA
Found at i:119705 original size:51 final size:50
Alignment explanation
Indices: 119630--119823 Score: 209
Period size: 51 Copynumber: 3.9 Consensus size: 50
119620 AAATTTCTAG
* * *
119630 ATTTTTCAT-CTCGGGGATACTCCAA-TCCCGGTTTAATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACA-CA
* * *
119680 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA-CA
* * *
119731 ATTTTCCATAATCGGGGATAGTCCAACTCCGATTTTATTTCCAAAACACTG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC-A
* * *
119782 ACTTTTCACAATCGGGGATACTCCAACCCCG---TTATTTCCAAA
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAA
119824 GGGATACTCC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
48 11 0.09
50 9 0.07
51 103 0.83
52 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (50 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACA
Found at i:123235 original size:18 final size:18
Alignment explanation
Indices: 123212--123249 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
123202 TATAATGTAT
*
123212 CATAGACAAAGAAAGGAA
1 CATAGACAAAGAAAGAAA
123230 CATAGACAAAGAAAGAAA
1 CATAGACAAAGAAAGAAA
123248 CA
1 CA
123250 ATATATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.63, C:0.13, G:0.18, T:0.05
Consensus pattern (18 bp):
CATAGACAAAGAAAGAAA
Found at i:124021 original size:42 final size:43
Alignment explanation
Indices: 123962--124047 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
123952 TTGTTAGATA
* *
123962 CCTAAATAGACTAAAAAAATACAAAAGCTATGCCA-TTGAAAG
1 CCTAAACAGACTAAAAAAATACAAAACCTATGCCATTTGAAAG
* *
124004 CCTAAACAGACTAAAAAAGTACAAAACCTATGGCATTTGAAAG
1 CCTAAACAGACTAAAAAAATACAAAACCTATGCCATTTGAAAG
124047 C
1 C
124048 TAACTTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 31 0.79
43 8 0.21
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (43 bp):
CCTAAACAGACTAAAAAAATACAAAACCTATGCCATTTGAAAG
Found at i:126534 original size:53 final size:54
Alignment explanation
Indices: 126469--126594 Score: 148
Period size: 56 Copynumber: 2.3 Consensus size: 54
126459 TACATTAGTC
* *** *
126469 TTTATCATATCTAGGTGTCAATTTTGTTAGA-GTAA-CCCCTAGCTATGTTGGAT
1 TTTATC-TATCTAGGTGCCAATTTCACTAGACGTAAGCCACTAGCTATGTTGGAT
*
126522 TTTATCTCATCTAGGTGCCAATTTCACTAGACTTAATGCCACTAGCTATGTTGGAT
1 TTTATCT-ATCTAGGTGCCAATTTCACTAGACGTAA-GCCACTAGCTATGTTGGAT
126578 TTTATCTTATCTAGGTG
1 TTTATC-TATCTAGGTG
126595 ACAGTCTCTA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
52 1 0.02
53 25 0.40
54 3 0.05
56 32 0.52
57 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (54 bp):
TTTATCTATCTAGGTGCCAATTTCACTAGACGTAAGCCACTAGCTATGTTGGAT
Found at i:126734 original size:56 final size:56
Alignment explanation
Indices: 126661--126783 Score: 151
Period size: 56 Copynumber: 2.2 Consensus size: 56
126651 AGTCTCATTC
*
126661 ACTTAACCCTAGCAGCTACA-TTAGGCTTTATCTCATATAGACACTAATTTAACTAG
1 ACTTAACCCTAGCAGCTA-AGTTAGGCTTAATCTCATATAGACACTAATTTAACTAG
* * * ** *
126717 ACTTAACCCTA-CTAGCTAAGTTGGGCTTAATTTCATCTAGGTACTAATTTCACTAG
1 ACTTAACCCTAGC-AGCTAAGTTAGGCTTAATCTCATATAGACACTAATTTAACTAG
126773 ACTTAACCCTA
1 ACTTAACCCTA
126784 ACAACAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
55 2 0.03
56 56 0.97
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (56 bp):
ACTTAACCCTAGCAGCTAAGTTAGGCTTAATCTCATATAGACACTAATTTAACTAG
Found at i:126796 original size:56 final size:56
Alignment explanation
Indices: 126703--126833 Score: 144
Period size: 56 Copynumber: 2.3 Consensus size: 56
126693 TCATATAGAC
* * **
126703 ACTAATTTAACTAGACTTAACCCTACTAGCTAAGTTGGGCT-TAATTTCATCTAGGT
1 ACTAATTTCACTAGACTTAACCCTACTAACTAAGTTGGGCTCT-AGCTCATCTAGGT
126759 ACTAATTTCACTAGACTTAACCCTAAC-AAC-AATGTTGGGCTCTAGCTCATCTAGGT
1 ACTAATTTCACTAGACTTAACCCT-ACTAACTAA-GTTGGGCTCTAGCTCATCTAGGT
* *
126815 CCCAATTTCA-TAAGACTTA
1 ACTAATTTCACT-AGACTTA
126834 CCATTGCCTG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 3 0.05
56 59 0.91
57 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (56 bp):
ACTAATTTCACTAGACTTAACCCTACTAACTAAGTTGGGCTCTAGCTCATCTAGGT
Found at i:129096 original size:13 final size:13
Alignment explanation
Indices: 129078--129113 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
129068 ATTTATTATG
129078 TATCGATACACTA
1 TATCGATACACTA
*
129091 TATCGATACACTG
1 TATCGATACACTA
129104 TATCGATACA
1 TATCGATACA
129114 TGAATAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACACTA
Found at i:129324 original size:53 final size:53
Alignment explanation
Indices: 129260--129396 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
129250 CTACTTCCAA
129260 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
129313 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
129366 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
129397 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:129429 original size:20 final size:20
Alignment explanation
Indices: 129366--129436 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
129356 GCCAATGTCC
**
129366 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
129386 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
129406 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
129426 TGTATCGATAC
1 TGTATCGATAC
129437 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:129502 original size:21 final size:21
Alignment explanation
Indices: 129476--129516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
129466 GTCAACCTTG
129476 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
129497 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
129517 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:131717 original size:21 final size:21
Alignment explanation
Indices: 131693--131744 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
131683 CAAAAATATT
** *
131693 TTAATTTAAATGTATTAAAAA
1 TTAATTTAAATAAAATAAAAA
131714 TTAATTT-AATAAAATAAAAA
1 TTAATTTAAATAAAATAAAAA
131734 TCTAATTTAAA
1 T-TAATTTAAA
131745 ATTTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.42
21 13 0.50
22 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATTTAAATAAAATAAAAA
Found at i:136032 original size:19 final size:18
Alignment explanation
Indices: 136008--136059 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
135998 CCACTTACCA
136008 CATGAAATGAAAGCAATG
1 CATGAAATGAAAGCAATG
* *
136026 CCATGAAATGAATGTAATG
1 -CATGAAATGAAAGCAATG
136045 CATGAAATGAAAGCA
1 CATGAAATGAAAGCA
136060 TGAAATGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (18 bp):
CATGAAATGAAAGCAATG
Found at i:136064 original size:8 final size:8
Alignment explanation
Indices: 136051--136094 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
136041 AATGCATGAA
136051 ATGAAAGC
1 ATGAAAGC
136059 ATGAAATGC
1 ATGAAA-GC
* *
136068 ATGTATGC
1 ATGAAAGC
*
136076 ATGAAGGC
1 ATGAAAGC
136084 ATGAAAGC
1 ATGAAAGC
136092 ATG
1 ATG
136095 GAATCATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.20
Consensus pattern (8 bp):
ATGAAAGC
Found at i:136251 original size:15 final size:14
Alignment explanation
Indices: 136223--136259 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
136213 ACATTCAGCC
136223 ATTTTTTTTGTTTG
1 ATTTTTTTTGTTTG
*
136237 ATTTTTTGTTTTTTG
1 ATTTTTT-TTGTTTG
136252 ATTTTTTT
1 ATTTTTTT
136260 GATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTGTTTG
Found at i:136278 original size:23 final size:23
Alignment explanation
Indices: 136223--136297 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
136213 ACATTCAGCC
136223 ATTTT-TTTTGTTTGATTTTTTGT-
1 ATTTTATTTT-TTTGATTTTTT-TA
*
136246 TTTTTGATTTTTTTGATTTTTTTA
1 ATTTT-ATTTTTTTGATTTTTTTA
* * *
136270 ATTTTATTTTCTTAATTTATTTA
1 ATTTTATTTTTTTGATTTTTTTA
136293 ATTTT
1 ATTTT
136298 TTTGATTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 25 0.57
24 15 0.34
25 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.07, T:0.76
Consensus pattern (23 bp):
ATTTTATTTTTTTGATTTTTTTA
Found at i:136305 original size:18 final size:17
Alignment explanation
Indices: 136228--136306 Score: 51
Period size: 18 Copynumber: 4.8 Consensus size: 17
136218 CAGCCATTTT
136228 TTTTGTTTGATTTTTT--
1 TTTT-TTTGATTTTTTAA
* *
136244 GTTTTTTGATTTTTTTGA
1 TTTTTTTGA-TTTTTTAA
*
136262 TTTTTTT-A-ATTTT-A
1 TTTTTTTGATTTTTTAA
* *
136276 TTTTCTTAATTTATTTAA
1 TTTTTTTGATTT-TTTAA
136294 TTTTTTTGATTTT
1 TTTTTTTGATTTT
136307 GAATTTTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.14
15 10 0.20
16 10 0.20
17 5 0.10
18 17 0.35
ACGTcount: A:0.15, C:0.01, G:0.08, T:0.76
Consensus pattern (17 bp):
TTTTTTTGATTTTTTAA
Found at i:136306 original size:9 final size:9
Alignment explanation
Indices: 136228--136274 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
136218 CAGCCATTTT
136228 TTTTGTTTGA
1 TTTT-TTTGA
136238 -TTTTTTG-
1 TTTTTTTGA
136245 -TTTTTTGA
1 TTTTTTTGA
136253 TTTTTTTGA
1 TTTTTTTGA
*
136262 TTTTTTTAA
1 TTTTTTTGA
136271 TTTT
1 TTTT
136275 ATTTTCTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.21
8 4 0.12
9 23 0.68
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:136306 original size:32 final size:33
Alignment explanation
Indices: 136228--136306 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
136218 CAGCCATTTT
* * * * *
136228 TTTTGTTTGATTTTTTGTTTTTTGATTTTTTTGA
1 TTTT-TTTGATTTTATGTTTCTTAATTTATTTAA
*
136262 TTTTTTTAATTTTAT-TTTCTTAATTTATTTAA
1 TTTTTTTGATTTTATGTTTCTTAATTTATTTAA
136294 TTTTTTTGATTTT
1 TTTTTTTGATTTT
136307 GAATTTTGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 25 0.66
33 9 0.24
34 4 0.11
ACGTcount: A:0.15, C:0.01, G:0.08, T:0.76
Consensus pattern (33 bp):
TTTTTTTGATTTTATGTTTCTTAATTTATTTAA
Found at i:136346 original size:39 final size:37
Alignment explanation
Indices: 136256--136346 Score: 85
Period size: 39 Copynumber: 2.3 Consensus size: 37
136246 TTTTTGATTT
* *
136256 TTTTGATTTTTTTAATTTTATTTTCTTAATTTATTTAA
1 TTTT-ATTTTTTGAATTTTATTTTCTTAAATTATTTAA
* *
136294 TTTTTTTGATTTTGAATTTTGATTTTCATTATAATT-TTTGA
1 TTTTATT--TTTTGAATTTT-ATTTTC-TTA-AATTATTTAA
136335 TTTTATTTTTTG
1 TTTTATTTTTTG
136347 TTAAAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
37 2 0.05
38 4 0.09
39 15 0.35
40 6 0.14
41 13 0.30
42 3 0.07
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (37 bp):
TTTTATTTTTTGAATTTTATTTTCTTAAATTATTTAA
Found at i:139382 original size:20 final size:20
Alignment explanation
Indices: 139340--139382 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
139330 CCATGTTTAG
* *
139340 AAATTTCAAAAAGCAACTGA
1 AAATTCCAAAAAGCAACTAA
*
139360 AAATTCCAAAAGGCAACTAA
1 AAATTCCAAAAAGCAACTAA
139380 AAA
1 AAA
139383 CTATTTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.16
Consensus pattern (20 bp):
AAATTCCAAAAAGCAACTAA
Found at i:139606 original size:15 final size:16
Alignment explanation
Indices: 139586--139620 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
139576 ATGCTCAATG
*
139586 AAATTACATTAA-TTA
1 AAATTAAATTAATTTA
139601 AAATTAAATTAATTTA
1 AAATTAAATTAATTTA
139617 AAAT
1 AAAT
139621 AGTGGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTAAATTAATTTA
Found at i:140864 original size:28 final size:28
Alignment explanation
Indices: 140803--140875 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
140793 TGTTAAGAGA
* *
140803 ATATTGTTTTCTTAAGATAACCTTATCC
1 ATATTGTCTTATTAAGATAACCTTATCC
** * *
140831 GCATTGTCTTATTAAGATATCTTTATCC
1 ATATTGTCTTATTAAGATAACCTTATCC
* *
140859 ATATTGCCTTATAAAGA
1 ATATTGTCTTATTAAGA
140876 CATCCCTATT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (28 bp):
ATATTGTCTTATTAAGATAACCTTATCC
Found at i:141866 original size:20 final size:20
Alignment explanation
Indices: 141841--141880 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
141831 ACTTATTTGA
141841 AAAAATACAA-AAAAAAAAAT
1 AAAAATA-AACAAAAAAAAAT
*
141861 AAAAATAAACAAAGAAAAAT
1 AAAAATAAACAAAAAAAAAT
141881 TGAGTGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (20 bp):
AAAAATAAACAAAAAAAAAT
Found at i:146129 original size:79 final size:78
Alignment explanation
Indices: 145988--146312 Score: 339
Period size: 79 Copynumber: 4.1 Consensus size: 78
145978 ATCCTTAACG
* * * ** *
145988 GTGAAAAATTGATGTTTTGGAAACAAACCGGGGTTGGAGTATCTTCTCAGAAATAACAGGGTTAG
1 GTGAAAAATCGATGTTTTAGAAATAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTAG
146053 AGTATCCCCCGATT
66 AGTAT-CCCCGATT
* *
146067 GTGAAAAATCGATGTTTTAGAAATACAGCCGGGGTTGGAGTATCCCCTC-GAAA-ATATGGGGTT
1 GTGAAAAATCGATGTTTTAGAAATA-AACCGGGGTTGGAGTATCCCCTCAGAAATA-ACGGGGTT
*
146130 AGAGTATCCCCGATG
64 AGAGTATCCCCGATT
* * * * * *
146145 GTGGAAAATCGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCTCCTCAGAAATAACGGGGTGA
1 GTGAAAAATCGATGTTTTAGAAAT-AAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTA
* *
146210 GAGTATCTCCAATT
65 GAGTATCCCCGATT
* * * * * * *
146224 GTGAAAAATTGATGTTTTAGAAATAAGGCCGAGGCTGGAGTATCCCCTCAAAAATAATGGGGTTG
1 GTGAAAAATCGATGTTTTAGAAATAA-ACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTA
** *
146289 GAGTATTTCCGATG
65 GAGTATCCCCGATT
*
146303 GTGGAAAATC
1 GTGAAAAATC
146313 AATATTTTGC
Statistics
Matches: 202, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
78 51 0.25
79 130 0.64
80 21 0.10
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (78 bp):
GTGAAAAATCGATGTTTTAGAAATAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTAG
AGTATCCCCGATT
Found at i:146263 original size:157 final size:158
Alignment explanation
Indices: 146000--146312 Score: 461
Period size: 158 Copynumber: 2.0 Consensus size: 158
145990 GAAAAATTGA
* * * *
146000 TGTTTTGGAAACAAACCGGGGTTGGAGTATCTTCTCAGAAATAACAGGGTTAGAGTATCCCCCGA
1 TGTTTTGGAAAAAAACCGGGGTTGGAGTATCTCCTCAGAAATAACAGGGTGAGAGTATCCCCCAA
* * *
146065 TTGTGAAAAATCGATGTTTTAGAAATACAGCCGGGGTTGGAGTATCCCCTCGAAAAT-ATGGGGT
66 TTGTGAAAAATCGATGTTTTAGAAATACAGCCGAGGCTGGAGTATCCCCTCAAAAATAATGGGGT
146129 TAGAGTATCCCCGATGGTGGAAAATCGG
131 TAGAGTATCCCCGATGGTGGAAAATCGG
* * *
146157 TGTTTTGGAAATAAAATCGGGGTTGGAGTATCTCCTCAGAAATAACGGGGTGAGAGTAT-CTCCA
1 TGTTTTGGAAA-AAAACCGGGGTTGGAGTATCTCCTCAGAAATAACAGGGTGAGAGTATCCCCCA
*
146221 ATTGTGAAAAATTGATGTTTTAGAAATA-AGGCCGAGGCTGGAGTATCCCCTCAAAAATAATGGG
65 ATTGTGAAAAATCGATGTTTTAGAAATACA-GCCGAGGCTGGAGTATCCCCTCAAAAATAATGGG
* **
146285 GTTGGAGTATTTCCGATGGTGGAAAATC
129 GTTAGAGTATCCCCGATGGTGGAAAATC
146313 AATATTTTGC
Statistics
Matches: 139, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
156 1 0.01
157 66 0.47
158 72 0.52
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (158 bp):
TGTTTTGGAAAAAAACCGGGGTTGGAGTATCTCCTCAGAAATAACAGGGTGAGAGTATCCCCCAA
TTGTGAAAAATCGATGTTTTAGAAATACAGCCGAGGCTGGAGTATCCCCTCAAAAATAATGGGGT
TAGAGTATCCCCGATGGTGGAAAATCGG
Found at i:148053 original size:24 final size:26
Alignment explanation
Indices: 148008--148059 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
147998 CCCTTTTGTT
*
148008 TTTTTTTTTTCACGTTGCGCTTGCTTC
1 TTTTTTTTTTCACATT-CGCTTGCTTC
*
148035 TTTTTTTTTT-ACATT-GCTTTCTTC
1 TTTTTTTTTTCACATTCGCTTGCTTC
148059 T
1 T
148060 CCCTTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
26 4 0.17
27 10 0.43
ACGTcount: A:0.06, C:0.19, G:0.10, T:0.65
Consensus pattern (26 bp):
TTTTTTTTTTCACATTCGCTTGCTTC
Found at i:148821 original size:3 final size:3
Alignment explanation
Indices: 148807--148848 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
148797 TTTATATATA
* *
148807 TAT TAA TAT TAT TAT T-T TTT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
148849 GATTTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:148836 original size:26 final size:28
Alignment explanation
Indices: 148796--148848 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
148786 ACGAATTTTC
148796 TTTTATATATATATTAATATTATTATTT
1 TTTTATATATATATTAATATTATTATTT
*
148824 TTTTAT-TAT-TATTATTATTATTATT
1 TTTTATATATATATTAATATTATTATT
148849 GATTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
27 3 0.12
28 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTATATATATATTAATATTATTATTT
Found at i:148865 original size:10 final size:9
Alignment explanation
Indices: 148847--148883 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
148837 ATTATTATTA
148847 TTGATTTTT
1 TTGATTTTT
148856 TTGAATTTTT
1 TTG-ATTTTT
*
148866 TTGATTTCT
1 TTGATTTTT
148875 TTGATTTTT
1 TTGATTTTT
148884 AATTTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.14, C:0.03, G:0.11, T:0.73
Consensus pattern (9 bp):
TTGATTTTT
Found at i:148871 original size:19 final size:18
Alignment explanation
Indices: 148847--148883 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
148837 ATTATTATTA
*
148847 TTGATTTTTTTGAATTTTT
1 TTGATTTCTTTG-ATTTTT
148866 TTGATTTCTTTGATTTTT
1 TTGATTTCTTTGATTTTT
148884 AATTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.14, C:0.03, G:0.11, T:0.73
Consensus pattern (18 bp):
TTGATTTCTTTGATTTTT
Found at i:152398 original size:20 final size:21
Alignment explanation
Indices: 152375--152443 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
152365 GCAAAAGCGT
152375 AAAAAATG-AAAA-AAAAAACA
1 AAAAAATGCAAAACAAAAAA-A
152395 AAAAAATGCAAAAGCAAAAAAA
1 AAAAAATGCAAAA-CAAAAAAA
* * *
152417 AAAAAAGGGAACAACAAAAATA
1 AAAAAATGCAA-AACAAAAAAA
152439 AAAAA
1 AAAAA
152444 TGAGGACATG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.19
21 4 0.10
22 22 0.52
23 8 0.19
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.04
Consensus pattern (21 bp):
AAAAAATGCAAAACAAAAAAA
Found at i:153780 original size:27 final size:27
Alignment explanation
Indices: 153736--154250 Score: 484
Period size: 27 Copynumber: 18.8 Consensus size: 27
153726 GACCTCTTCA
* * *
153736 AAGTCCACGATTCAGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
153763 AAGTCCACAACTCGGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
153790 AAGTCAACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
153817 AAGTCCACAACTCCATGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
153844 AAAATCCACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
153872 AAGTCCACAACTCCGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* * * * *
153900 AAGCCCACAAGTCAGTGGCACCCTTTCA
1 AAGTCCACAACTCCGTGGCATCCTTT-T
* * * ** *
153928 AAGCCCATAAGTAAGTGGCACCCCTTTTT
1 AAGTCCACAACTCCGTGGCA-TCC-TTTT
* * * *
153957 AAGCCCGCAACTCTGTGGCA-CTCTTTA
1 AAGTCCACAACTCCGTGGCATC-CTTTT
*
153984 AAGTCCATAACTCCGTGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
154010 AAAGTCCACAACTCC-TGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
* * *
154037 AAGTTCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
154064 AGGTCCACAACTCCGTGGC-TCTCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTTT
154091 AAAGTCCACAACTCCGTGGCA-CTCTTTT
1 -AAGTCCACAACTCCGTGGCATC-CTTTT
* * * *
154119 AAAGACCTACCACTTCGTGGCACCCTTTT
1 -AAGTCC-ACAACTCCGTGGCATCCTTTT
* *
154148 AGGTCTACAACTCCGTGGCA-CCTATTT
1 AAGTCCACAACTCCGTGGCATCCT-TTT
* *
154175 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
** * *
154202 AAGTCCACAACTCTATGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
154229 AAGTCTACAAGTCCGTGGCATC
1 AAGTCCACAACTCCGTGGCATC
154251 ATTTCAAAGC
Statistics
Matches: 415, Mismatches: 57, Indels: 32
0.82 0.11 0.06
Matches are distributed among these distances:
26 25 0.06
27 247 0.60
28 104 0.25
29 35 0.08
30 4 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:153975 original size:57 final size:53
Alignment explanation
Indices: 153750--154200 Score: 211
Period size: 55 Copynumber: 8.2 Consensus size: 53
153740 CCACGATTCA
* * * * ** * * *
153750 GTGGCATCCTTTTAAGTCCACAACTCGGTGGCATCTTTTTAAGTCAACAACTCC
1 GTGGCACCCTTTAAAGCCCATAACTAAGTGGCACCTTTTTAAGCCCACAACT-C
* * * * * * **
153804 GTGGCATCCTTTTAAGTCCACAACTCCA-TGGCATCCTTTTAAAATCCACAACTCC
1 GTGGCACCCTTTAAAGCCCATAACT-AAGTGGCA-CCTTTTTAAGCCCACAACT-C
* * * * ** *
153859 GTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGCCCACAAGTC
1 GTGGCACCCTTTAAAGCCCATAACTAAGTGGCA-CCTTTTTAAGCCCACAACTC
* *
153913 AGTGGCACCCTTTCAAAGCCCATAAGTAAGTGGCACCCCTTTTTAAGCCCGCAACTC
1 -GTGGCACCCTTT-AAAGCCCATAACTAAGTGGCA--CCTTTTTAAGCCCACAACTC
* * ** * *
153970 TGTGGCACTCTTTAAAGTCCATAACTCCGTGGCACCTTTTAAAGTCCACAACTC
1 -GTGGCACCCTTTAAAGCCCATAACTAAGTGGCACCTTTTTAAGCCCACAACTC
* * ** * ** * * *
154024 CTGGCACCCTTTTAAGTTCACAACTCTGTGGCACCCTTTTAGGTCCACAACTCC
1 GTGGCACCCTTTAAAGCCCATAACTAAGTGGCACCTTTTTAAGCCCACAACT-C
* * * * ** * * *
154078 GTGGCTCTCTTTTAAAGTCCACAACTCCGTGGCACTCTTTTAAAGACCTACCACTTC
1 GTGGCAC-CCTTTAAAGCCCATAACTAAGTGGCAC-CTTTTTAAG-CCCACAAC-TC
* * * * * ** * *
154135 GTGGCACCCTTTTAGGTCTACAACTCCGTGGCACCTATTTAAGTCCACAACTC
1 GTGGCACCCTTTAAAGCCCATAACTAAGTGGCACCTTTTTAAGCCCACAACTC
154188 TGTGGCACCCTTT
1 -GTGGCACCCTTT
154201 TAAGTCCACA
Statistics
Matches: 325, Mismatches: 60, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
53 45 0.14
54 72 0.22
55 105 0.32
56 61 0.19
57 41 0.13
58 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.29
Consensus pattern (53 bp):
GTGGCACCCTTTAAAGCCCATAACTAAGTGGCACCTTTTTAAGCCCACAACTC
Found at i:154268 original size:28 final size:28
Alignment explanation
Indices: 154235--154849 Score: 604
Period size: 28 Copynumber: 21.1 Consensus size: 28
154225 TTTAAAGTCT
* *
154235 ACAAGTCCGTGGCATCATTTCAAAGCCT
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* * * *
154263 ACAAGTTAGTGGTAACCTTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
154291 ACAAGTCCA-TGGCATCATTTCAAAGCCC
1 ACAAGT-CAGTGGCATCATTTCAAAGCCC
*
154319 ACAAGTCAGTGGCACCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* *
154347 ACAAGTTAATGGCATCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
154375 ACAAGTCAGTGGCAACTCATTTCAAAGCCC
1 ACAAGTCAGTGGC-A-TCATTTCAAAGCCC
* *
154405 ACATAAGTCAGTGGCAACTCATTTGAAAACCTAC
1 AC--AAGTCAGTGGC-A-TCATTTCAAAGCC--C
* *
154439 ACAAGTC-GATAGCAACCCATTTCAAAGCCCAC
1 ACAAGTCAG-TGGC-A-TCATTTCAAAG-CC-C
* * *
154471 ACAAGTCATTGGCAACCCATTTTAAAGCCC
1 ACAAGTCAGTGGC-A-TCATTTCAAAGCCC
*
154501 ACAAGTTAGTGGCATCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* *
154529 ATAAGTCCGTGGCATCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* *
154557 ACAAGTCGGTGGCACCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
*
154585 ACAAGTCAGTGGCATCATTTCAAAGCCA
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* * * * *
154613 AAAAGTTAATGGCACCATTCCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
*
154641 ACAAGTCAGTGGCATCATTTAAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
*
154669 ACAAGTCAGTGACATCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* *
154697 ATAAGTCAGTGGCATCCTTTCAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* * *
154725 ATAAGTCTGTGGCATCATTTTAAAGCCC
1 ACAAGTCAGTGGCATCATTTCAAAGCCC
* *
154753 ACAAGTCGGTGGCAACTCATTTCAAAACCCAC
1 ACAAGTCAGTGGC-A-TCATTTC-AAAGCC-C
* * *
154785 ACAAGTCAATGGCAACTTATTTGAAAGCCCAC
1 ACAAGTCAGTGGC-A-TCATTTCAAAG-CC-C
* * *
154817 ACAAGTCGGTGGCAACCCTTTTCAAAGCCC
1 ACAAGTCAGTGGC-A-TCATTTCAAAGCCC
154847 ACA
1 ACA
154850 CAAGTCGGTG
Statistics
Matches: 498, Mismatches: 73, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
27 2 0.00
28 322 0.65
29 4 0.01
30 38 0.08
31 13 0.03
32 114 0.23
33 2 0.00
34 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (28 bp):
ACAAGTCAGTGGCATCATTTCAAAGCCC
Found at i:155009 original size:64 final size:64
Alignment explanation
Indices: 154364--155065 Score: 380
Period size: 64 Copynumber: 11.6 Consensus size: 64
154354 AATGGCATCA
* * * * * *
154364 TTTCAAAG-CC-CACAAGTCAGTGGCAAC-TCATTTCAAAGCCCACATAAGTCAGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACAT-TTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * * * *** **
154426 TTTGAAAACCTACACAAGTCGATAGCAACCCATTTCAAAGCCCACACAAGTCATTGGCAACCCAT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCC-T
** * * * * *
154491 TTT-AAAG-CC-CACAAGTTAGTGGCATCA--TTTCAAAG-CC-CATAAGTCCGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * *
154546 TTTCAAAG-CC-CACAAGTCGGTGGCACCA--TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* *** * * * * *
154602 TTTCAAAG-CCA-AAAAGTTAATGGCACCA--TTCCAAAG-CC-CACAAGTCAGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * * * * *
154658 TTTAAAAG-CC-CACAAGTCAGTGACATCA--TTTCAAAG-CC-CATAAGTCAGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * * *
154714 TTTCAAAG-CC-CATAAGTCTGTGGCATCA-TTTT-AAAG-CC-CACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* ** *
154772 TTTCAAAACCCACACAAGTCAATGGCAAC-TTATTTGAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATT-TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * * *
154836 TTTCAAAGCCCACACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGCAACCTT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * * *
154900 TTTCAAAGCCCACACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGGAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * ** * *
154964 TTT-AAAGCCCACACAAGTTGGTGGCATCATTTTTCAAAAGTCCACAC-TTTCAGTAGC-ACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTC-AAAGCCCACACAAGTCGGTGGCAACCC-
155026 T
64 T
* * * *
155027 TTTTAAAGCGCACACAAGTCAGTGGCAACCTTTTTCAAA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAA
155066 TCACCACTTT
Statistics
Matches: 533, Mismatches: 85, Indels: 43
0.81 0.13 0.07
Matches are distributed among these distances:
55 3 0.01
56 184 0.35
57 7 0.01
58 18 0.03
59 4 0.01
60 22 0.04
61 3 0.01
62 26 0.05
63 42 0.08
64 220 0.41
65 4 0.01
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (64 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
Found at i:155009 original size:96 final size:96
Alignment explanation
Indices: 154752--155010 Score: 328
Period size: 96 Copynumber: 2.7 Consensus size: 96
154742 TTTTAAAGCC
* * * ** *
154752 CACAAGTCGGTGGCAA-CTCATTTCAAAACCCACACAAGTCAATGGCAAC-TTATTTGAAAGCCC
1 CACAAGTCGGTGGGAACCTC-TCTCAAAGCCCACACAAGTCGGTGGCAACATT-TTTCAAAGCCC
*
154815 ACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
64 ACACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
*
154848 CACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCAAAGCCCAC
1 CACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCAC
*
154913 ACAAGTCGGTGGGAA-CCTCTCTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCT-TCTCAAAGCCCA
* * * * *
154944 CACAAGTCGGTGGGAACC-CTTTTAAAGCCCACACAAGTTGGTGGCATCATTTTTCAAAAGTCCA
1 CACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGCAACATTTTTC-AAAGCCCA
155008 CAC
65 CAC
155011 TTTCAGTAGC
Statistics
Matches: 145, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
95 35 0.24
96 105 0.72
97 5 0.03
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (96 bp):
CACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCAC
ACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
Found at i:155035 original size:95 final size:94
Alignment explanation
Indices: 154752--155061 Score: 300
Period size: 96 Copynumber: 3.2 Consensus size: 94
154742 TTTTAAAGCC
* * * * ** *
154752 CACAAGTCGGTGGCAACTCATTTCAAAACCCACACAAGTCAATGGCAAC-TTATTTGAAAGCCCA
1 CACAAGTCGGTGGGAAC-CCTTTTAAAGCCCACACAAGTCGGTGGCAACATT-TTTCAAAGCCCA
* *
154816 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
64 CACAAGTCAGTAGC-ACCCTTTTCAAAGCCCA
* * *
154848 CACAAGTCGGTGGGAACCTCTCTCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCAAAGCCCAC
1 CACAAGTCGGTGGGAACC-CTTTTAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCAC
* * * * *
154913 ACAAGTCGGTGGGAACCTCTCTCAAAGCCCA
65 ACAAGTCAGTAGCACCCT-TTTCAAAGCCCA
* * *
154944 CACAAGTCGGTGGGAACCCTTTTAAAGCCCACACAAGTTGGTGGCATCATTTTTCAAAAGTCCAC
1 CACAAGTCGGTGGGAACCCTTTTAAAGCCCACACAAGTCGGTGGCAACATTTTTC-AAAGCCCAC
** * *
155009 AC-TTTCAGTAGCACCCATTTTTAAAGCGCA
65 ACAAGTCAGTAGCACCC-TTTTCAAAGCCCA
* * *
155039 CACAAGTCAGTGGCAACCTTTTT
1 CACAAGTCGGTGGGAACCCTTTT
155062 CAAATCACCA
Statistics
Matches: 181, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
95 74 0.41
96 105 0.58
97 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (94 bp):
CACAAGTCGGTGGGAACCCTTTTAAAGCCCACACAAGTCGGTGGCAACATTTTTCAAAGCCCACA
CAAGTCAGTAGCACCCTTTTCAAAGCCCA
Found at i:162548 original size:15 final size:14
Alignment explanation
Indices: 162528--162576 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 14
162518 ATGTTGTCCT
*
162528 AAAAAAGCAAAAAA
1 AAAAAAACAAAAAA
162542 AAAAAAACAAAAACA
1 AAAAAAACAAAAA-A
162557 AAAAAAACACACAAAA
1 AAAAAAACA-A-AAAA
162573 AAAA
1 AAAA
162577 GTACAAAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 12 0.39
15 10 0.32
16 6 0.19
17 3 0.10
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:162561 original size:19 final size:19
Alignment explanation
Indices: 162537--162573 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
162527 TAAAAAAGCA
162537 AAAAAAAAAAAACAAAAAC
1 AAAAAAAAAAAACAAAAAC
* *
162556 AAAAAAAACACACAAAAA
1 AAAAAAAAAAAACAAAAA
162574 AAAGTACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAACAAAAAC
Found at i:163892 original size:32 final size:32
Alignment explanation
Indices: 163856--164075 Score: 261
Period size: 31 Copynumber: 6.9 Consensus size: 32
163846 ATCTCTCTTC
* *
163856 TCAAAGTCCACAACTTAGTGGCATCTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTCT
*
163888 TCAAAGTCCACAACTCAGTGGCATCTCTTTTC-
1 TCAAAGTCCACGACTCAGTGGCATCT-TTTTCT
* *
163920 T--AAGTCCACGACTCAATGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTCT
* * * *
163950 TCCAAGTCCATGACTCAATGGCATCTTTTTTTT
1 TCAAAGTCCACGACTCAGTGGCATC-TTTTTCT
* *
163983 TAAAAGTCCACGACTCAGTAGCATC-TTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTCT
164014 TCAAAGTCCACGACTCAGTGGCATC-TTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTCT
* *
164045 TCAAAGTCCACAACTCCGTGGCATCCTTTTT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTT
164076 AAGCCCACAA
Statistics
Matches: 164, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
29 5 0.03
30 21 0.13
31 56 0.34
32 48 0.29
33 34 0.21
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (32 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTTCT
Found at i:163999 original size:95 final size:94
Alignment explanation
Indices: 163856--164054 Score: 265
Period size: 95 Copynumber: 2.1 Consensus size: 94
163846 ATCTCTCTTC
** * * * *
163856 TCAAAGTCCACAACTTAGTGGCATCTTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTT-TTC
1 TCAAAGTCCATGACTCAATGGCATCTTTTTCTTAAAAGTCCACAACTCAGTAGCATCTCTTCTTC
*
163920 TAAGTCCACGACTCAATGGCATCCTTTTCT
66 AAAGTCCACGACTCAATGGCAT-CTTTTCT
* * * *
163950 TCCAAGTCCATGACTCAATGGCATCTTTTTTTTTAAAAGTCCACGACTCAGTAGCATCTTTTCTT
1 TCAAAGTCCATGACTCAATGGCATC-TTTTTCTTAAAAGTCCACAACTCAGTAGCATCTCTTCTT
*
164015 CAAAGTCCACGACTCAGTGGCATCTTTTCT
65 CAAAGTCCACGACTCAATGGCATCTTTTCT
164045 TCAAAGTCCA
1 TCAAAGTCCA
164055 CAACTCCGTG
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 20 0.22
95 47 0.52
96 23 0.26
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (94 bp):
TCAAAGTCCATGACTCAATGGCATCTTTTTCTTAAAAGTCCACAACTCAGTAGCATCTCTTCTTC
AAAGTCCACGACTCAATGGCATCTTTTCT
Found at i:164138 original size:29 final size:29
Alignment explanation
Indices: 164052--164153 Score: 109
Period size: 28 Copynumber: 3.6 Consensus size: 29
164042 TCTTCAAAGT
* * *
164052 CCACAACTCCGTGGCA-TCCTTTTTAAGC
1 CCACAAGTCAGTGGCACCCCTTTTTAAGC
* **
164080 CCACAAGTTAGTGGCA-CCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCCTTTTTAAGC
*
164108 CCATAAGTCAGTGGCACCCCTTTTTAAGC
1 CCACAAGTCAGTGGCACCCCTTTTTAAGC
* *
164137 CCACAACTCTGTGGCAC
1 CCACAAGTCAGTGGCAC
164154 TCTTTAAAGT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 36 0.60
29 24 0.40
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (29 bp):
CCACAAGTCAGTGGCACCCCTTTTTAAGC
Done.