Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008333.1 Hibiscus syriacus cultivar Beakdansim tig00111046_pilon, whole genome shotgun sequence
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: 371579
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3385 original size:34 final size:34
Alignment explanation
Indices: 3324--3402 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
3314 ATGGTGATGA
* *
3324 AATGGTAATGGAAAGGATGATGTTATGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATGGCGTGAT
3358 -ATGGTGATGGAATATGG-TGATGATATGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATGGCGTGAT
3392 AAT-GTGATGGA
1 AATGGTGATGGA
3403 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 11 0.28
34 25 0.62
35 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (34 bp):
AATGGTGATGGAAAGGATGATGATATGGCGTGAT
Found at i:13256 original size:25 final size:22
Alignment explanation
Indices: 13207--13256 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 22
13197 AAACAAAATC
**
13207 AAAGCACTCAAAGAAGAAATTG
1 AAAGCACTCAAAGAAGAAAAAG
13229 AAAGCACTCAAAAAGGAAGAAAAAG
1 AAAGCACTC--AAA-GAAGAAAAAG
13254 AAA
1 AAA
13257 TGAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
24 3 0.13
25 11 0.48
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (22 bp):
AAAGCACTCAAAGAAGAAAAAG
Found at i:23230 original size:24 final size:21
Alignment explanation
Indices: 23196--23238 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
23186 TGCACAAGAT
*
23196 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
23218 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
23239 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:25551 original size:18 final size:19
Alignment explanation
Indices: 25530--25583 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
25520 CATTTGGTCA
25530 AAAG-CATGTATTTTCATT
1 AAAGTCATGTATTTTCATT
* *
25548 AAAGTCTTGTTTTTTCATT
1 AAAGTCATGTATTTTCATT
*
25567 AAAAATCATGTCATTTT
1 -AAAGTCATGT-ATTTT
25584 AGGAAGGTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 8 0.29
21 4 0.14
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (19 bp):
AAAGTCATGTATTTTCATT
Found at i:28288 original size:24 final size:21
Alignment explanation
Indices: 28253--28295 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
28243 GGCTCATTCT
*
28253 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
28276 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
28296 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:30711 original size:24 final size:24
Alignment explanation
Indices: 30684--30739 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
30674 AGAGAACATT
30684 CTTTGGAATACCAAATGTTCCAAC
1 CTTTGGAATACCAAATGTTCCAAC
*
30708 CTTTGGAATACCAAATGTTCGAAC
1 CTTTGGAATACCAAATGTTCCAAC
30732 CTTTGGAA
1 CTTTGGAA
30740 CTTCAATGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (24 bp):
CTTTGGAATACCAAATGTTCCAAC
Found at i:32258 original size:36 final size:36
Alignment explanation
Indices: 32211--32293 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
32201 GATACAATCT
* *
32211 GTCCATCACCATTATCACGCCTATGTCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
32247 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
*
32283 TTCCATCACCA
1 GTCCATCACCA
32294 ACTTATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACACCTATATCATCACCATA
Found at i:32273 original size:11 final size:11
Alignment explanation
Indices: 32214--32293 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 11
32204 ACAATCTGTC
32214 CATCACCATTAT
1 CATCACCA-TAT
* *
32226 CA-CGCCTATGT
1 CATCACC-ATAT
32237 CATCACCATAGT
1 CATCACCATA-T
32249 CCATCACCATTAT
1 -CATCACCA-TAT
32262 CA-CACCTATAT
1 CATCACC-ATAT
32273 CATCACCATATT
1 CATCACCATA-T
32285 CCATCACCA
1 -CATCACCA
32294 ACTTATAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
11 21 0.38
12 15 0.27
13 17 0.31
14 2 0.04
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:32755 original size:14 final size:15
Alignment explanation
Indices: 32732--32776 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
32722 TTTGGAGTGC
32732 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
32747 AAAAG-AAGAAAAGC
1 AAAAGAAAGAAAAGA
32761 AAAAGCAAAAGAAAAG
1 AAAAG--AAAGAAAAG
32777 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 13 0.50
15 5 0.19
17 8 0.31
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:36657 original size:19 final size:20
Alignment explanation
Indices: 36633--36675 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36623 AGCATTTATC
* *
36633 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATA
36652 TTCATTAAAAATCATGTATA
1 TTCATTAAAAATCATGTATA
36672 TTCA
1 TTCA
36676 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATA
Found at i:37698 original size:18 final size:16
Alignment explanation
Indices: 37656--37710 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
37646 GTAAGTTATC
37656 TTCATTTTTCTTACTAT
1 TTCATTTTTCTTA-TAT
37673 TTCA-TTTTCTTATACT
1 TTCATTTTTCTTATA-T
37689 TTCATCTTTTCTTAT-T
1 TTCAT-TTTTCTTATAT
37705 TTCATT
1 TTCATT
37711 ACTTTATCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.09
16 19 0.54
17 4 0.11
18 9 0.26
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (16 bp):
TTCATTTTTCTTATAT
Found at i:37722 original size:25 final size:25
Alignment explanation
Indices: 37676--37728 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
37666 TTACTATTTC
*
37676 ATTTTCTTATACTTTCATCTTTTCTT
1 ATTTTCATATACTTTCATCTTTT-TT
37702 ATTTTCAT-TACTTT-ATCCTTTTTT
1 ATTTTCATATACTTTCAT-CTTTTTT
37726 ATT
1 ATT
37729 AACCTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 11 0.44
26 7 0.28
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTTTCATATACTTTCATCTTTTTT
Found at i:42510 original size:16 final size:16
Alignment explanation
Indices: 42478--42523 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
42468 ATAGTAATGA
42478 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
42496 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
42512 AGTAAGAAAATG
1 AATAAGAAAATG
42524 GAGATAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 3 0.12
18 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:46535 original size:13 final size:12
Alignment explanation
Indices: 46476--46537 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 12
46466 TCTTTTTGAA
46476 TTTCTCTTTTTCT
1 TTTCT-TTTTTCT
46489 TTTCTTTTCTTCT
1 TTTCTTTT-TTCT
46502 TTTCAGATTTTTTTCT
1 TTTC----TTTTTTCT
*
46518 CTTCTTTTTGTCT
1 TTTCTTTTT-TCT
46531 TTTCTTT
1 TTTCTTT
46538 CTTTTTGCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
12 8 0.20
13 22 0.54
16 7 0.17
17 4 0.10
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:46542 original size:29 final size:30
Alignment explanation
Indices: 46475--46543 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
46465 CTCTTTTTGA
*
46475 ATTTCTCTTTTTCTTTTCTTTTCTTCTTTTC
1 ATTTCT-TTTTTCTCTTCTTTTCTTCTTTTC
**
46506 AGAT-TTTTTTCTCTTCTTTT-TGTCTTTTC
1 ATTTCTTTTTTCTCTTCTTTTCT-TCTTTTC
46535 -TTTCTTTTT
1 ATTTCTTTTT
46544 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 2 0.06
29 26 0.84
30 1 0.03
31 2 0.06
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (30 bp):
ATTTCTTTTTTCTCTTCTTTTCTTCTTTTC
Found at i:46871 original size:14 final size:14
Alignment explanation
Indices: 46852--46878 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46842 ATGAAATAAA
46852 TAGAGGAAGAACAT
1 TAGAGGAAGAACAT
46866 TAGAGGAAGAACA
1 TAGAGGAAGAACA
46879 ACAAAGAACA
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:0.52, C:0.07, G:0.30, T:0.11
Consensus pattern (14 bp):
TAGAGGAAGAACAT
Found at i:62550 original size:24 final size:24
Alignment explanation
Indices: 62523--62574 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
62513 GACATGTCCT
* * *
62523 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
62547 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
62571 TTGA
1 TTGA
62575 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:66313 original size:11 final size:11
Alignment explanation
Indices: 66293--66325 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
66283 TAACATTGGT
66293 TCTTCTTTGAG
1 TCTTCTTTGAG
*
66304 TCTTCGTTGAG
1 TCTTCTTTGAG
66315 TCTTCTTTGAG
1 TCTTCTTTGAG
66326 ATACTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.52
Consensus pattern (11 bp):
TCTTCTTTGAG
Found at i:66807 original size:27 final size:27
Alignment explanation
Indices: 66745--66799 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
66735 CTAAATAATG
*
66745 GAAACAAAGAAATTAAAATCCAAAGAA
1 GAAACAAAGAAATCAAAATCCAAAGAA
*
66772 GAAACAAAGAAATCAAAATGCAAAGAA
1 GAAACAAAGAAATCAAAATCCAAAGAA
66799 G
1 G
66800 TGCCAAAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (27 bp):
GAAACAAAGAAATCAAAATCCAAAGAA
Found at i:69903 original size:11 final size:11
Alignment explanation
Indices: 69883--69915 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
69873 TAACATTGGT
69883 TCTTCTTTGAG
1 TCTTCTTTGAG
*
69894 TCTTCGTTGAG
1 TCTTCTTTGAG
69905 TCTTCTTTGAG
1 TCTTCTTTGAG
69916 ATACTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.52
Consensus pattern (11 bp):
TCTTCTTTGAG
Found at i:73468 original size:11 final size:11
Alignment explanation
Indices: 73448--73480 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
73438 TAACATTGGT
73448 TCTTCTTTGAG
1 TCTTCTTTGAG
*
73459 TCTTCGTTGAG
1 TCTTCTTTGAG
73470 TCTTCTTTGAG
1 TCTTCTTTGAG
73481 ATACTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.52
Consensus pattern (11 bp):
TCTTCTTTGAG
Found at i:77909 original size:10 final size:10
Alignment explanation
Indices: 77894--77946 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 10
77884 TTTTTTTCAA
77894 AAAAAAAAAC
1 AAAAAAAAAC
77904 AAAAAAAAAGGC
1 AAAAAAAAA--C
77916 AAAAAAAAAAGAAC
1 ---AAAAAAA-AAC
77930 AAAAAAAAAC
1 AAAAAAAAAC
77940 AAAAAAA
1 AAAAAAA
77947 GGCCAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
10 19 0.51
11 7 0.19
12 1 0.03
14 1 0.03
15 7 0.19
16 2 0.05
ACGTcount: A:0.87, C:0.08, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:77930 original size:26 final size:23
Alignment explanation
Indices: 77892--77946 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 23
77882 ATTTTTTTTC
77892 AAAAAAAAAAACAAAAAAAAAGGCA
1 AAAAAAAAAAACAAAAAAAAA--CA
77917 AAAAAAAAAGAACAAAAAAAAACA
1 AAAAAAAAA-AACAAAAAAAAACA
77941 AAAAAA
1 AAAAAA
77947 GGCCAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 8 0.28
25 9 0.31
26 12 0.41
ACGTcount: A:0.87, C:0.07, G:0.05, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAACAAAAAAAAACA
Found at i:77946 original size:13 final size:13
Alignment explanation
Indices: 77892--77938 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
77882 ATTTTTTTTC
77892 AAAAAAAAAAAC-
1 AAAAAAAAAAACA
**
77904 AAAAAAAAAGGCA
1 AAAAAAAAAAACA
77917 AAAAAAAAAGAACA
1 AAAAAAAAA-AACA
77931 AAAAAAAA
1 AAAAAAAA
77939 CAAAAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 10 0.34
13 9 0.31
14 10 0.34
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:86214 original size:13 final size:13
Alignment explanation
Indices: 86192--86221 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
86182 ACTAAACACC
86192 TTTC-ACATACCT
1 TTTCAACATACCT
86204 TTTCAACATACCT
1 TTTCAACATACCT
86217 TTTCA
1 TTTCA
86222 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:86620 original size:16 final size:15
Alignment explanation
Indices: 86594--86645 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
86584 GAGATGTAAG
86594 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
86608 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
86624 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
86641 CTTAT
1 -TTAT
86646 TTTATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:92772 original size:27 final size:28
Alignment explanation
Indices: 92712--92772 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
92702 AAGAAAATCG
*
92712 GAAAAGAAATTGAAGCACTCCAAAAGAA
1 GAAAAGAAATTGAAGCACTCAAAAAGAA
* *
92740 -AGAAAGAAATT-TAGCATTCAAAAAGAA
1 GA-AAAGAAATTGAAGCACTCAAAAAGAA
92767 GAAAAG
1 GAAAAG
92773 CAAAGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.59, C:0.10, G:0.18, T:0.13
Consensus pattern (28 bp):
GAAAAGAAATTGAAGCACTCAAAAAGAA
Found at i:99903 original size:13 final size:11
Alignment explanation
Indices: 99881--99946 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
99871 TATCACGCCT
99881 ATATCATCACC
1 ATATCATCACC
99892 ATAGTCCATCACC
1 ATA-T-CATCACC
*
99905 ATTATCA-CGCC
1 A-TATCATCACC
99916 TATATCATCACC
1 -ATATCATCACC
99928 ATATTCCATCACC
1 ATA-T-CATCACC
99941 ATATCA
1 ATATCA
99947 CGCCTGTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:99909 original size:36 final size:36
Alignment explanation
Indices: 99863--99963 Score: 159
Period size: 36 Copynumber: 2.8 Consensus size: 36
99853 CAATCTGTCT
*
99863 ATCATCATTATCACGCCTATATCATCACCATAGTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
*
99899 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
* *
99935 ATCACCA-TATCACGCCTGTATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
99964 ACTTATAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 20 0.33
36 41 0.67
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCC
Found at i:110086 original size:24 final size:24
Alignment explanation
Indices: 110059--110108 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
110049 TCCCATAATT
110059 CGTTATCCATATTATTACCAAATC
1 CGTTATCCATATTATTACCAAATC
110083 CGTTATCCATATTATTACCAAATC
1 CGTTATCCATATTATTACCAAATC
110107 CG
1 CG
110109 AGTCTTCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (24 bp):
CGTTATCCATATTATTACCAAATC
Found at i:110379 original size:12 final size:13
Alignment explanation
Indices: 110356--110380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
110346 ACATACAACG
110356 AAAATACAAAAAA
1 AAAATACAAAAAA
110369 AAAATACAAAAA
1 AAAATACAAAAA
110381 GAAGTTCAAG
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:114051 original size:24 final size:24
Alignment explanation
Indices: 114024--114073 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
114014 TCCCATAATT
114024 CGTTATCCATATTATTACCAAATC
1 CGTTATCCATATTATTACCAAATC
114048 CGTTATCCATATTATTACCAAATC
1 CGTTATCCATATTATTACCAAATC
114072 CG
1 CG
114074 AGTCTTCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (24 bp):
CGTTATCCATATTATTACCAAATC
Found at i:119671 original size:33 final size:33
Alignment explanation
Indices: 119629--119697 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
119619 GTTGATGAAT
119629 GAAGGATGAT-TTAATGGAGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGAG-TGAAATGGTAATG
* * * *
119662 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGAGTGAAATGGTAATG
119695 GAA
1 GAA
119698 TATGATGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.29
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGAGTGAAATGGTAATG
Found at i:132180 original size:15 final size:15
Alignment explanation
Indices: 132160--132195 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
132150 AAAAAAAAAG
132160 ATGAAAGAATAAGAA
1 ATGAAAGAATAAGAA
*
132175 ATGAAATAATAAGAA
1 ATGAAAGAATAAGAA
132190 AGTGAA
1 A-TGAA
132196 GATAACTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (15 bp):
ATGAAAGAATAAGAA
Found at i:132893 original size:36 final size:36
Alignment explanation
Indices: 132823--132924 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
132813 AATGGAAGGA
* * * * *
132823 TGATGTTATTGGCATGAT-ATGATGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
132858 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
132894 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
132925 ATATTGTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 15 0.25
36 46 0.75
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:152884 original size:17 final size:17
Alignment explanation
Indices: 152862--152894 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
152852 GTAGGAGTCT
152862 TTTTCTTTTCTCTTTTG
1 TTTTCTTTTCTCTTTTG
*
152879 TTTTCTTTTTTCTTTT
1 TTTTCTTTTCTCTTTT
152895 TTCTTTTTTT
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:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTCTCTTTTG
Found at i:152891 original size:19 final size:18
Alignment explanation
Indices: 152859--152905 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
152849 GATGTAGGAG
*
152859 TCTTTTTCTTTTCTCTTT
1 TCTTTTTTTTTTCTCTTT
* *
152877 TGTTTTCTTTTTTCTTTTT
1 TCTTTT-TTTTTTCTCTTT
152896 TCTTTTTTTT
1 TCTTTTTTTT
152906 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
TCTTTTTTTTTTCTCTTT
Found at i:152891 original size:24 final size:23
Alignment explanation
Indices: 152861--152905 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
152851 TGTAGGAGTC
152861 TTTTTCTTTTCTCTTTTGTTTTCT
1 TTTTTCTTTTCTCTTTT-TTTTCT
*
152885 TTTTTCTTTTTTCTTTTTTTT
1 TTTTTCTTTTCTCTTTTTTTT
152906 GTTGTAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTCTCTTTTTTTTCT
Found at i:152903 original size:7 final size:7
Alignment explanation
Indices: 152879--152903 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
152869 TTCTCTTTTG
152879 TTTTCTT
1 TTTTCTT
152886 TTTTCTT
1 TTTTCTT
152893 TTTTCTT
1 TTTTCTT
152900 TTTT
1 TTTT
152904 TTGTTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:152904 original size:17 final size:17
Alignment explanation
Indices: 152861--152905 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
152851 TGTAGGAGTC
*
152861 TTTTTCTTTTCTCTTTT
1 TTTTTCTTTTTTCTTTT
*
152878 GTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
152895 TTCTTT-TTTTT
1 TT-TTTCTTTTT
152906 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTT
Found at i:153312 original size:13 final size:12
Alignment explanation
Indices: 153293--153378 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
153283 ATATAGGCGT
153293 GATATGGTGATG
1 GATATGGTGATG
153305 GAATATGGTGAT-
1 G-ATATGGTGATG
*
153317 GATATAGGCG-T-
1 GATAT-GGTGATG
153328 GATAATGGTGATG
1 GAT-ATGGTGATG
153341 GACTATGGTGAT-
1 GA-TATGGTGATG
*
153353 GATATAGG-CAT-
1 GATAT-GGTGATG
153364 GATAATGGTGATG
1 GAT-ATGGTGATG
153377 GA
1 GA
153379 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:153348 original size:36 final size:36
Alignment explanation
Indices: 153275--153379 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
153265 ATTTATAAGT
* *
153275 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
153310 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
153346 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
153380 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:154392 original size:33 final size:33
Alignment explanation
Indices: 154331--154398 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
154321 GTTGATGAAT
*
154331 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
154364 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
154397 GA
1 GA
154399 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:158386 original size:12 final size:13
Alignment explanation
Indices: 158369--158398 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
158359 GTTGTAGGAG
158369 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
158381 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
158394 TCTTT
1 TCTTT
158399 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:158815 original size:33 final size:33
Alignment explanation
Indices: 158754--158821 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
158744 GTTGATGAAT
*
158754 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
158787 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
158820 GA
1 GA
158822 CATATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:176340 original size:14 final size:15
Alignment explanation
Indices: 176321--176352 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
176311 CATTTACTTT
176321 ATATATG-TATTATA
1 ATATATGTTATTATA
176335 ATATATGTTATTATA
1 ATATATGTTATTATA
176350 ATA
1 ATA
176353 CATATCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
ATATATGTTATTATA
Found at i:185166 original size:24 final size:23
Alignment explanation
Indices: 185138--185198 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
185128 ACTTTTCTTT
185138 CTTTCTTTTTCTTCTTTTTGAGTA
1 CTTTCTTTTTCTTC-TTTTGAGTA
** *
185162 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTA
*
185185 CTTTGATTTTTCTT
1 CTTT-CTTTTTCTT
185199 TGTTGGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.64
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTA
Found at i:187130 original size:35 final size:35
Alignment explanation
Indices: 187089--187194 Score: 212
Period size: 35 Copynumber: 3.0 Consensus size: 35
187079 CATTCACATG
187089 TTAGTATAAATTATCATATTATTATTTCCATCCTA
1 TTAGTATAAATTATCATATTATTATTTCCATCCTA
187124 TTAGTATAAATTATCATATTATTATTTCCATCCTA
1 TTAGTATAAATTATCATATTATTATTTCCATCCTA
187159 TTAGTATAAATTATCATATTATTATTTCCATCCTA
1 TTAGTATAAATTATCATATTATTATTTCCATCCTA
187194 T
1 T
187195 GCTTATTTGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (35 bp):
TTAGTATAAATTATCATATTATTATTTCCATCCTA
Found at i:190200 original size:24 final size:21
Alignment explanation
Indices: 190166--190211 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
190156 TCCACAAGAT
*
190166 ATGTCCTTTGACATTTCAAAAG
1 ATGTCCTTTGA-AATTCAAAAG
190188 ATGTACCTCTTGAAATTCAAAAG
1 ATGT-CCT-TTGAAATTCAAAAG
190211 A
1 A
190212 ATGAGCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAAG
Found at i:202961 original size:34 final size:34
Alignment explanation
Indices: 202922--203024 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
202912 TTGATGAATG
*
202922 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTTAATGGCG-TGAAATGGTAATGGA
* * *
202956 AAGGATGATGTTATTGGCGTGATATGGTGATGGA
1 AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
* *
202990 ATATGG-TGATGAT-ATGGCGTGATAATGGTGATGGA
1 A-A-GGATGATGTTAATGGCGTGA-AATGGTAATGGA
203025 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.53
35 25 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (34 bp):
AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
Found at i:203018 original size:35 final size:35
Alignment explanation
Indices: 202944--203024 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 35
202934 ATGGTGATGA
* *
202944 AATGGTAATGGAAAGGATGATGTTATTGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
202979 -ATGGTGATGGAATATGG-TGATGATA-TGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATTGGCGTGAT
203013 AATGGTGATGGA
1 AATGGTGATGGA
203025 CAGATTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 20 0.49
35 19 0.46
36 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
Found at i:206401 original size:34 final size:33
Alignment explanation
Indices: 206340--206442 Score: 93
Period size: 34 Copynumber: 3.0 Consensus size: 33
206330 TTGATGAATG
* * *
206340 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTT-ATGGCG-TGATATGGTGATGGA
*
206374 AAGGATGATGTTATTGGCGTGATATGGTGATAGA
1 AAGGATGATGTTA-TGGCGTGATATGGTGATGGA
*
206408 ATATGG-TGATGATATGGCGTGATAATGGTGATGGA
1 A-A-GGATGATGTTATGGCGTGAT-ATGGTGATGGA
206443 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
34 32 0.55
35 24 0.41
36 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.35, T:0.31
Consensus pattern (33 bp):
AAGGATGATGTTATGGCGTGATATGGTGATGGA
Found at i:224916 original size:10 final size:10
Alignment explanation
Indices: 224901--224930 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
224891 GATGTCAAAG
224901 GTAGCTGAAT
1 GTAGCTGAAT
224911 GTAGCTGAAT
1 GTAGCTGAAT
*
224921 GTAGATGAAT
1 GTAGCTGAAT
224931 ATGCTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (10 bp):
GTAGCTGAAT
Found at i:235997 original size:16 final size:16
Alignment explanation
Indices: 235976--236007 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
235966 TCTTCCACCA
235976 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
235992 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
236008 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:253437 original size:24 final size:25
Alignment explanation
Indices: 253379--253439 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
253369 ACTTTTCTTT
253379 CTTTC-TTTTTCTTCTTTTCGAGTA
1 CTTTCATTTTTCTTCTTTTCGAGTA
* *
253403 CTTTCA-ATTTCTTCTTTT-GAGTG
1 CTTTCATTTTTCTTCTTTTCGAGTA
*
253426 CTTTGATTTTTCTT
1 CTTTCATTTTTCTT
253440 TGCTGGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 9 0.29
24 22 0.71
ACGTcount: A:0.10, C:0.18, G:0.10, T:0.62
Consensus pattern (25 bp):
CTTTCATTTTTCTTCTTTTCGAGTA
Found at i:258373 original size:24 final size:21
Alignment explanation
Indices: 258339--258384 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
258329 TCCACAAGAT
*
258339 ATGTCCTTTGACATTTCAAAAG
1 ATGTCCTTTGA-AATTCAAAAG
258361 ATGTACCTCTTGAAATTCAAAAG
1 ATGT-CCT-TTGAAATTCAAAAG
258384 A
1 A
258385 ATGAGCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAAG
Found at i:287101 original size:14 final size:13
Alignment explanation
Indices: 287082--287131 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
287072 AAGCAAAAAG
287082 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
287096 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
287109 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
287120 AAAGAAAAAGAA
1 AAAGAAAAAGAA
287132 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:287128 original size:19 final size:18
Alignment explanation
Indices: 287071--287131 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
287061 ATTGGCGTAC
*
287071 AAAGCAAAAAG-AAAGAA
1 AAAGAAAAAAGAAAAGAA
287088 AAAGACAAAAAGAAGAAG-A
1 AAAGA-AAAAAGAA-AAGAA
287107 AAAGAAGAAAAGAAAAGAA
1 AAAGAA-AAAAGAAAAGAA
287126 AAAGAA
1 AAAGAA
287132 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.11
18 10 0.26
19 21 0.55
20 3 0.08
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAGAA
Found at i:291986 original size:20 final size:21
Alignment explanation
Indices: 291961--292014 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
291951 TTTTTTTTCA
291961 AAAAAAAACAAAAAAAAAA-C
1 AAAAAAAACAAAAAAAAAAGC
**
291981 AAAAAAGGCAAAAAAAAAAGGC
1 AAAAAAAACAAAAAAAAAA-GC
292003 AAAAAAAA-AAAA
1 AAAAAAAACAAAA
292015 GAGCCAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.61
21 4 0.14
22 7 0.25
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAGC
Found at i:291993 original size:15 final size:14
Alignment explanation
Indices: 291975--292013 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
291965 AAAACAAAAA
291975 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
291990 -AAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
292003 AAAAAAAAAAA
1 AAAAAAAAAAA
292014 AGAGCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:291996 original size:12 final size:13
Alignment explanation
Indices: 291976--292012 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
291966 AAACAAAAAA
291976 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
291990 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
292003 AAAAAAAAAA
1 AAAAAAAAAA
292013 AAGAGCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:292014 original size:15 final size:15
Alignment explanation
Indices: 291974--292025 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
291964 AAAAACAAAA
291974 AAAAAACAAAAAAGGC
1 AAAAAA-AAAAAAGGC
291990 --AAAAAAAAAAGGC
1 AAAAAAAAAAAAGGC
292003 AAAAAAAAAAAAGAGCC
1 AAAAAAAAAAAAG-G-C
292020 AAAAAA
1 AAAAAA
292026 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 11 0.34
16 1 0.03
17 7 0.22
ACGTcount: A:0.79, C:0.10, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGGC
Found at i:295908 original size:42 final size:46
Alignment explanation
Indices: 295820--295920 Score: 113
Period size: 50 Copynumber: 2.2 Consensus size: 46
295810 AGGATCAGAT
*
295820 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAG-TTA
1 TTATTATTTTATTAGGAATTAA-G--GGGTTAAAAC-A-ATGTTTAGTTTA
295870 TTATTATTTTATTAGGAATT-A-GGGTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGGGTTAAAACAATGTTTAGTTTA
295913 TTA-TATTT
1 TTATTATTT
295921 ATTCTTTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
42 12 0.24
43 6 0.12
45 10 0.20
49 1 0.02
50 20 0.41
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGGGTTAAAACAATGTTTAGTTTA
Found at i:299239 original size:33 final size:33
Alignment explanation
Indices: 299178--299245 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
299168 GTTGATGAAT
*
299178 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
299211 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
299244 GA
1 GA
299246 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:303670 original size:33 final size:33
Alignment explanation
Indices: 303609--303676 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
303599 GTTGATGAAT
*
303609 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
303642 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
303675 GA
1 GA
303677 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:306360 original size:5 final size:5
Alignment explanation
Indices: 306350--306375 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
306340 CTTCAACTTC
306350 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
306376 CTTTTGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:309425 original size:11 final size:11
Alignment explanation
Indices: 309409--309444 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
309399 TTATGTATGA
*
309409 AAATGGTGAAT
1 AAATGGTGAAG
309420 AAATGGTGAAG
1 AAATGGTGAAG
*
309431 AAATGATGAAG
1 AAATGGTGAAG
309442 AAA
1 AAA
309445 AGAAGGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (11 bp):
AAATGGTGAAG
Found at i:314831 original size:13 final size:12
Alignment explanation
Indices: 314812--314897 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
314802 ATATAGGCGT
314812 GATATGGTGATG
1 GATATGGTGATG
314824 GAATATGGTGAT-
1 G-ATATGGTGATG
*
314836 GATATAGGCG-T-
1 GATAT-GGTGATG
314847 GATAATGGTGATG
1 GAT-ATGGTGATG
314860 GACTATGGTGAT-
1 GA-TATGGTGATG
*
314872 GATATAGGCG-T-
1 GATAT-GGTGATG
314883 GATAATGGTGATG
1 GAT-ATGGTGATG
314896 GA
1 GA
314898 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:314867 original size:36 final size:36
Alignment explanation
Indices: 314794--314898 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
314784 ATTTATAAGT
* *
314794 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
314829 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
314865 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
314899 ATATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:317802 original size:13 final size:14
Alignment explanation
Indices: 317784--317822 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
317774 GATGTAGGAG
317784 TCTTTTTGTTTTC-
1 TCTTTTTGTTTTCT
317797 TC-TTTTGTTTTCT
1 TCTTTTTGTTTTCT
317810 TCTTTCTTGTTTT
1 TCTTT-TTGTTTT
317823 TTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.43
13 4 0.17
14 2 0.09
15 7 0.30
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (14 bp):
TCTTTTTGTTTTCT
Found at i:318273 original size:36 final size:36
Alignment explanation
Indices: 318198--318302 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
318188 TTTATAAGTT
* * * *
318198 GGTGATAATATAGGTGTGAT-ATGGTGATGGAAAAT
1 GGTGATGATATAGGCGTGATAATGGTGATGGACAAC
* *
318233 GGTGATGATATAGGCGTGATAATGGTGACGGACTAC
1 GGTGATGATATAGGCGTGATAATGGTGATGGACAAC
318269 GGTGATGATATAGGCGTGATAATGGTGATGGACA
1 GGTGATGATATAGGCGTGATAATGGTGATGGACA
318303 GATTGTATCT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
35 18 0.30
36 43 0.70
ACGTcount: A:0.30, C:0.06, G:0.36, T:0.28
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGTGATGGACAAC
Found at i:320492 original size:32 final size:34
Alignment explanation
Indices: 320468--320550 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
320458 TGGTAAGGGA
320468 ATGATGATGATATAGGTGTGAATGGTGATAGAAG
1 ATGATGATGATATAGGTGTGAATGGTGATAGAAG
* *
320502 ATGGTGATGATATAGGTGTGCAATGGTGATGGAAG
1 ATGATGATGATATAGGTGTG-AATGGTGATAGAAG
*
320537 ATGGTGATGA-ATAG
1 ATGATGATGATATAG
320551 ATAGTATCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 23 0.50
35 23 0.50
ACGTcount: A:0.33, C:0.01, G:0.37, T:0.29
Consensus pattern (34 bp):
ATGATGATGATATAGGTGTGAATGGTGATAGAAG
Found at i:320512 original size:34 final size:35
Alignment explanation
Indices: 320472--320550 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
320462 AAGGGAATGA
320472 TGATGATATAGGTGTG-AATGGTGATAGAAGATGG
1 TGATGATATAGGTGTGCAATGGTGATAGAAGATGG
*
320506 TGATGATATAGGTGTGCAATGGTGATGGAAGATGG
1 TGATGATATAGGTGTGCAATGGTGATAGAAGATGG
320541 TGATGA-ATAG
1 TGATGATATAG
320551 ATAGTATCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 20 0.47
35 23 0.53
ACGTcount: A:0.32, C:0.01, G:0.38, T:0.29
Consensus pattern (35 bp):
TGATGATATAGGTGTGCAATGGTGATAGAAGATGG
Found at i:321206 original size:30 final size:31
Alignment explanation
Indices: 321170--321229 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
321160 CTTAGCTTTA
**
321170 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
321200 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
321230 GGAAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:322152 original size:19 final size:20
Alignment explanation
Indices: 322128--322178 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
322118 CGGCCAAGAG
* *
322128 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
322147 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
322167 CATGTATTTTCA
1 CATGTATTTTCA
322179 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:322615 original size:19 final size:20
Alignment explanation
Indices: 322591--322630 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
322581 TATCCTTTAT
322591 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
322610 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
322630 T
1 T
322631 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:326724 original size:30 final size:31
Alignment explanation
Indices: 326672--326731 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
326662 CTTAGCTTTA
**
326672 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
326702 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
326732 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:327680 original size:20 final size:20
Alignment explanation
Indices: 327641--327711 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
327631 CGGCCAAGAG
* *
327641 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
327660 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
327680 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
327700 CATGTATTTTCA
1 CATGTATTTTCA
327712 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 12 0.24
20 37 0.76
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:330912 original size:30 final size:31
Alignment explanation
Indices: 330860--330919 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
330850 CTTAGCTTTA
**
330860 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
330890 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
330920 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:331763 original size:19 final size:20
Alignment explanation
Indices: 331739--331789 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
331729 CAGCCAAGAG
* *
331739 CATGTATATTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
331758 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
331778 CATGTATTTTCA
1 CATGTATTTTCA
331790 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:334364 original size:13 final size:13
Alignment explanation
Indices: 334346--334371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
334336 TTATAGGCGT
334346 GAAAATGGTGATG
1 GAAAATGGTGATG
334359 GAAAATGGTGATG
1 GAAAATGGTGATG
334372 AACAGATAGT
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:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:334744 original size:19 final size:20
Alignment explanation
Indices: 334706--334748 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
334696 CGGTTAAGGT
*
334706 TGAAAACACATGACTTTTAA
1 TGAAAACACATGAATTTTAA
*
334726 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
334745 TGAA
1 TGAA
334749 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:337635 original size:34 final size:35
Alignment explanation
Indices: 337596--337676 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 35
337586 ATGGTGATGA
* *
337596 AATGGTAATGGAA-A-GGATGATGTTATTAGCGTGAT
1 AATGGTGATGGAATATGG-TGATGATA-TAGCGTGAT
*
337631 -ATGGTGATGGAATATGGTGATGATATGGCGTGAT
1 AATGGTGATGGAATATGGTGATGATATAGCGTGAT
337665 AATGGTGATGGA
1 AATGGTGATGGA
337677 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 19 0.47
35 19 0.47
36 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAATATGGTGATGATATAGCGTGAT
Found at i:342097 original size:34 final size:34
Alignment explanation
Indices: 342058--342160 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
342048 TTGATGAATG
*
342058 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTTAATGGCG-TGAAATGGTAATGGA
* * *
342092 AAGGATGATGTTATTGGCGTGATATGGTGATGGA
1 AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
* *
342126 ATATGG-TGATGAT-ATGGCGTGATAATGGTGATGGA
1 A-A-GGATGATGTTAATGGCGTGA-AATGGTAATGGA
342161 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.53
35 25 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (34 bp):
AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
Found at i:342154 original size:35 final size:35
Alignment explanation
Indices: 342080--342160 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 35
342070 ATGGTGATGA
* *
342080 AATGGTAATGGAAAGGATGATGTTATTGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
342115 -ATGGTGATGGAATATGG-TGATGATA-TGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATTGGCGTGAT
342149 AATGGTGATGGA
1 AATGGTGATGGA
342161 CAGATTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 20 0.49
35 19 0.46
36 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
Found at i:344496 original size:13 final size:14
Alignment explanation
Indices: 344475--344515 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
344465 AAAAAAACAA
344475 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
344490 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
344504 AAAAAAACAAAA
1 AAAAAAA-AAAA
344516 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:344515 original size:20 final size:20
Alignment explanation
Indices: 344492--344536 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
344482 AAAAAGGCAA
*
344492 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
344512 AAAAAAAGAGCCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
344532 CAAAA
1 AAAAA
344537 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.78, C:0.13, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:344536 original size:8 final size:8
Alignment explanation
Indices: 344456--344518 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
344446 ATTTTTTTTT
344456 CAAAAAAA
1 CAAAAAAA
344464 CAAAAAAA
1 CAAAAAAA
344472 C-AAAAAA
1 CAAAAAAA
344479 CAAAAAAA
1 CAAAAAAA
344487 GGC-AAAAAA
1 --CAAAAAAA
**
344496 -AAAAAGG
1 CAAAAAAA
344503 CAAAAAAA
1 CAAAAAAA
344511 CAAAAAAA
1 CAAAAAAA
344519 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 11 0.24
8 28 0.61
9 6 0.13
10 1 0.02
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:349905 original size:6 final size:6
Alignment explanation
Indices: 349894--349937 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
349884 GATGTAGGAG
*
349894 TCTTTT TC-TTT TCTTTT TCTTTT TCTTCTT TTTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
349938 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 19 0.58
7 9 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:349910 original size:11 final size:10
Alignment explanation
Indices: 349896--349938 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
349886 TGTAGGAGTC
349896 TTTTTCTTTT
1 TTTTTCTTTT
349906 CTTTTTC-TTT
1 -TTTTTCTTTT
*
349916 TTCTTCTTTT
1 TTTTTCTTTT
349926 TTTTTCTCTTT
1 TTTTTCT-TTT
349937 TT
1 TT
349939 GTTGCTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 5 0.18
10 12 0.43
11 11 0.39
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:349917 original size:12 final size:12
Alignment explanation
Indices: 349894--349937 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
349884 GATGTAGGAG
349894 TCTTTTTC-TTT
1 TCTTTTTCTTTT
349905 TCTTTTTCTTTT
1 TCTTTTTCTTTT
*
349917 TCTTCTTTTTTTT
1 TCTT-TTTCTTTT
349930 TCTCTTTT
1 TCT-TTTT
349938 TGTTGCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 8 0.28
12 7 0.24
13 13 0.45
14 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:349947 original size:21 final size:20
Alignment explanation
Indices: 349899--349937 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
349889 AGGAGTCTTT
349899 TTCTTTTCTTTTTCTTTTTC
1 TTCTTTTCTTTTTCTTTTTC
349919 TTCTTTT-TTTTTCTCTTTT
1 TTCTTTTCTTTTTCT-TTTT
349938 TGTTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTCTTTTCTTTTTCTTTTTC
Found at i:350787 original size:19 final size:20
Alignment explanation
Indices: 350749--350791 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
350739 GAAACCCCTT
*
350749 TGAAAACACATGACTTTTAA
1 TGAAAACACATGAATTTTAA
*
350769 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
350788 TGAA
1 TGAA
350792 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:353389 original size:24 final size:23
Alignment explanation
Indices: 353331--353390 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
353321 AAAATCAGCA
*
353331 AAGAAAATAAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
353354 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
353378 AAGAAAAGGAAAG
1 AAGAAAATGAAAG
353391 AAATAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.10, G:0.20, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:354644 original size:24 final size:21
Alignment explanation
Indices: 354610--354652 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
354600 TGCACAAGAT
*
354610 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
354632 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
354653 AGAATGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:356555 original size:13 final size:11
Alignment explanation
Indices: 356514--356598 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
356504 ACAATCTGTC
356514 CATCACCATTAT
1 CATCACCA-TAT
*
356526 CA-CGCCTATAT
1 CATCACC-ATAT
356537 CATCACCATAGT
1 CATCACCATA-T
356549 CCATCACCATTAT
1 -CATCACCA-TAT
*
356562 CA-CGCCTATAT
1 CATCACC-ATAT
356573 CATCACCATATT
1 CATCACCATA-T
356585 CCATCACCATAT
1 -CATCACCATAT
356597 CA
1 CA
356599 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:356558 original size:36 final size:36
Alignment explanation
Indices: 356511--356612 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
356501 GATACAATCT
356511 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
356547 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
356583 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
356613 TCCTTCCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:356627 original size:33 final size:34
Alignment explanation
Indices: 356512--356628 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
356502 ATACAATCTG
* *
356512 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
356546 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
356584 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
356617 TCCATTACCATT
1 TCCATCACCATT
356629 TCATCACCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:356646 original size:33 final size:33
Alignment explanation
Indices: 356512--356651 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
356502 ATACAATCTG
* * *
356512 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACACCAATAACATCATCC-T
* * *
356546 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACACCAATAACATCATCC---T
*
356584 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACACCAATAACATCATCCT
* * *
356617 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CACCAATAACATCATCCT
356650 TC
1 TC
356652 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACACCAATAACATCATCCT
Found at i:357031 original size:24 final size:24
Alignment explanation
Indices: 356991--357037 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
356981 AAAGTGCTAC
356991 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
357016 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
357038 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:360977 original size:13 final size:11
Alignment explanation
Indices: 360936--361019 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 11
360926 ACAATATGTC
360936 CATCACCATTAT
1 CATCACCA-TAT
*
360948 CA-CGCCTATAT
1 CATCACC-ATAT
360959 CATCACCATAGT
1 CATCACCATA-T
360971 CCATCACCAT-T
1 -CATCACCATAT
*
360982 -ATCACGCCTAAT
1 CATCAC-CAT-AT
360994 CATCACCATATT
1 CATCACCATA-T
361006 CCATCACCATAT
1 -CATCACCATAT
361018 CA
1 CA
361020 CGCCAATAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
9 5 0.09
10 2 0.03
11 15 0.26
12 12 0.21
13 24 0.41
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:361003 original size:35 final size:36
Alignment explanation
Indices: 360933--361033 Score: 161
Period size: 35 Copynumber: 2.9 Consensus size: 36
360923 GATACAATAT
360933 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
360969 GTCCATCACCATTATCACGCCTA-ATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
361004 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
361034 TCCTTCCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 10 0.16
35 28 0.46
36 23 0.38
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:365601 original size:23 final size:23
Alignment explanation
Indices: 365573--365627 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
365563 GTGATGGAAT
365573 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
365596 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
365619 ATGGTGATG
1 ATGGTGATG
365628 GACAGATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Done.