Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008813.1 Hibiscus syriacus cultivar Beakdansim tig00111975_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: 252071
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8816 original size:13 final size:13
Alignment explanation
Indices: 8798--8823 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8788 AACTTTGGCT
8798 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
8811 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
8824 CCTCTCTTTT
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:12532 original size:17 final size:17
Alignment explanation
Indices: 12507--12547 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12497 CATAACACTC
*
12507 AAAAGAAAATTAAAAGT
1 AAAAGAAAAATAAAAGT
*
12524 AAAATAAAAATAAAAG-
1 AAAAGAAAAATAAAAGT
12540 -AAAGAAAA
1 AAAAGAAAA
12548 TTCAACAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAGAAAAATAAAAGT
Found at i:13415 original size:11 final size:11
Alignment explanation
Indices: 13401--13425 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13391 TTTTTTTGCC
13401 TTTTTTTGTTT
1 TTTTTTTGTTT
13412 TTTTTTTGTTT
1 TTTTTTTGTTT
13423 TTT
1 TTT
13426 GAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:15484 original size:20 final size:22
Alignment explanation
Indices: 15455--15494 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
15445 AGGAGAGTTT
15455 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
15475 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
15495 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:16725 original size:27 final size:28
Alignment explanation
Indices: 16664--16725 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
16654 AAAGAAAATC
*
16664 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
16692 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
16719 AGAAAAG
1 AGAAAAG
16726 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:18036 original size:24 final size:21
Alignment explanation
Indices: 18002--18047 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
17992 TCCATAAGAC
*
18002 ATGTCCTTTGACATTTCAAAAG
1 ATGTCCTTTGA-AATTCAAAAG
18024 ATGTACCTCTTGAAATTCAAAAG
1 ATGT-CCT-TTGAAATTCAAAAG
18047 A
1 A
18048 ATGTGCCAAT
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:18060 original size:24 final size:23
Alignment explanation
Indices: 18016--18061 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
18006 CCTTTGACAT
**
18016 TTCAAAAGATGTACCTCTTGAAA
1 TTCAAAAGATGTACCAATTGAAA
*
18039 TTCAAAAGAATGTGCCAATTGAA
1 TTCAAAAG-ATGTACCAATTGAA
18062 GTACCAAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (23 bp):
TTCAAAAGATGTACCAATTGAAA
Found at i:25305 original size:19 final size:20
Alignment explanation
Indices: 25281--25320 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
25271 TATCCTTTCT
25281 TTATTTAATTTCATT-CTTA
1 TTATTTAATTTCATTACTTA
*
25300 TTATTTATTTTCATTACTTA
1 TTATTTAATTTCATTACTTA
25320 T
1 T
25321 ATTATTATCC
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:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTAATTTCATTACTTA
Found at i:25642 original size:17 final size:17
Alignment explanation
Indices: 25614--25647 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
25604 CAAGTGCTGC
25614 AACAAGAAAGAAGAAAAA
1 AACAAGAAAGAA-AAAAA
25632 AACAA-AAAGAAAAAAA
1 AACAAGAAAGAAAAAAA
25648 GAATACTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (17 bp):
AACAAGAAAGAAAAAAA
Found at i:29087 original size:19 final size:20
Alignment explanation
Indices: 29063--29105 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29053 AGCATTTATC
*
29063 TTCA-TTAAAATTATGTATT
1 TTCATTTAAAATCATGTATT
*
29082 TTCATTTAAAATCATGTGTT
1 TTCATTTAAAATCATGTATT
29102 TTCA
1 TTCA
29106 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (20 bp):
TTCATTTAAAATCATGTATT
Found at i:29467 original size:13 final size:13
Alignment explanation
Indices: 29449--29474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29439 ACTATCTGTT
29449 CATCACCATTTTC
1 CATCACCATTTTC
29462 CATCACCATTTTC
1 CATCACCATTTTC
29475 ACGCCTATAA
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:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:29697 original size:16 final size:16
Alignment explanation
Indices: 29678--29732 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
29668 CATTTCTATC
29678 CATTTCCTTTTCTTAT
1 CATTTCCTTTTCTTAT
29694 CATTTCCTTTCTTCTT-T
1 CATTTCC-TT-TTCTTAT
29711 CATATT-CTTTT-TTAAT
1 CAT-TTCCTTTTCTT-AT
29727 CATTTC
1 CATTTC
29733 TTTCTTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 13 0.39
17 7 0.21
18 7 0.21
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCCTTTTCTTAT
Found at i:29740 original size:16 final size:16
Alignment explanation
Indices: 29692--29746 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
29682 TCCTTTTCTT
29692 ATCATTTCCTTTCTTCT-
1 ATCATTT-CTTTCTT-TA
*
29709 TTCATATTCTTT-TTTA
1 ATCAT-TTCTTTCTTTA
29725 ATCATTTCTTTCTTTA
1 ATCATTTCTTTCTTTA
29741 AT-ATTT
1 ATCATTT
29747 GCATATTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.33
16 12 0.36
17 8 0.24
18 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (16 bp):
ATCATTTCTTTCTTTA
Found at i:34937 original size:13 final size:13
Alignment explanation
Indices: 34915--34944 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
34905 ACTAAACACC
34915 TTTC-ACATACCT
1 TTTCAACATACCT
34927 TTTCAACATACCT
1 TTTCAACATACCT
34940 TTTCA
1 TTTCA
34945 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:37707 original size:15 final size:15
Alignment explanation
Indices: 37672--37700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37662 GTACTTCAAC
37672 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
37686 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
37701 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:39974 original size:20 final size:20
Alignment explanation
Indices: 39949--39995 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39939 TTATTGGTGG
39949 GCTGGTTAACCTCTTCACTA
1 GCTGGTTAACCTCTTCACTA
*
39969 GCTGGTTAACCTCTTTACTA
1 GCTGGTTAACCTCTTCACTA
39989 GCTGGTT
1 GCTGGTT
39996 GGTGAGCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (20 bp):
GCTGGTTAACCTCTTCACTA
Found at i:46130 original size:13 final size:14
Alignment explanation
Indices: 46105--46139 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46095 AAAAATTCAG
46105 AAAAGAAGAAAATA
1 AAAAGAAGAAAATA
* *
46119 AAAAGAAGAAATTC
1 AAAAGAAGAAAATA
46133 AAAAGAA
1 AAAAGAA
46140 AGCAAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (14 bp):
AAAAGAAGAAAATA
Found at i:46412 original size:46 final size:48
Alignment explanation
Indices: 46314--46415 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 48
46304 AGGATTAGAT
*
46314 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAACATTATTTTTTAGTTA
1 TTATTATTTTATTAGGAATT-A--ATGAGTTAAAACATTATTGTTTAGTTA
*
46365 TTATTATTTTATTAGGAATT-A-GAGTTAAGACATGT-TTAGTTTA-TTA
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACAT-TATT-GTTTAGTTA
46411 TTATT
1 TTATT
46416 GTATTCATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
46 21 0.45
47 6 0.13
51 20 0.43
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (48 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACATTATTGTTTAGTTA
Found at i:47859 original size:19 final size:21
Alignment explanation
Indices: 47815--47867 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
47805 GAAACTCCTT
47815 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGA-TTTTTAAA
47837 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
47856 TGAAGATACATG
1 TGAAAATACATG
47868 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:56112 original size:18 final size:17
Alignment explanation
Indices: 56091--56140 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
56081 TTGAAATTTC
56091 TTTTTTCTTTTCTGAATT
1 TTTTTTCTTTT-TGAATT
**
56109 TTTTCTTCTTTTTGTCTT
1 TTTT-TTCTTTTTGAATT
56127 TTTCTTTCTTTTTG
1 TTT-TTTCTTTTTG
56141 CACTCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTGAATT
Found at i:56909 original size:19 final size:21
Alignment explanation
Indices: 56865--56917 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
56855 GAATCCCCTT
56865 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGA-TTTTTAAA
56887 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
56906 TGAAGATACATG
1 TGAAAATACATG
56918 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:63431 original size:11 final size:11
Alignment explanation
Indices: 63403--63472 Score: 52
Period size: 13 Copynumber: 6.0 Consensus size: 11
63393 CTTGGCTTTG
63403 CTTTTCTTTTT
1 CTTTTCTTTTT
***
63414 GAATTCTTTTT
1 CTTTTCTTTTT
63425 CTTTTCTTTTCTT
1 CTTTTC-TTT-TT
63438 CTTTTCTTCTTCT
1 CTTTTCTT-TT-T
*
63451 TTTTGTCTTTTT
1 CTTT-TCTTTTT
63463 C-TTTCTTTTT
1 CTTTTCTTTTT
63473 GCACTCCAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
10 7 0.15
11 13 0.28
12 7 0.15
13 15 0.33
14 4 0.09
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:63441 original size:19 final size:18
Alignment explanation
Indices: 63417--63472 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
63407 TCTTTTTGAA
63417 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
63435 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
63454 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
63472 T
1 T
63473 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:68237 original size:17 final size:17
Alignment explanation
Indices: 68217--68249 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
68207 TAAAATAGAG
68217 AGGAAATTGATGTATTT
1 AGGAAATTGATGTATTT
68234 AGGAAATTGATGTATT
1 AGGAAATTGATGTATT
68250 ATGGATCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (17 bp):
AGGAAATTGATGTATTT
Found at i:69033 original size:15 final size:15
Alignment explanation
Indices: 69013--69048 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
69003 ACTGCAAAAG
69013 AGAAGGAATCTGGCT
1 AGAAGGAATCTGGCT
69028 AGAAGGAATCTGGCT
1 AGAAGGAATCTGGCT
69043 A-AAGGA
1 AGAAGGA
69049 GACGTGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.39, C:0.11, G:0.33, T:0.17
Consensus pattern (15 bp):
AGAAGGAATCTGGCT
Found at i:72100 original size:2 final size:2
Alignment explanation
Indices: 72088--72134 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
72078 CAAAACAAAC
72088 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72131 AT AT
1 AT AT
72135 CGTGCAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73921 original size:19 final size:20
Alignment explanation
Indices: 73880--73933 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
73870 AATTCCTTTT
* *
73880 AAAATACATGATTTTTAATG
1 AAAATACATGATCTTTAACG
73900 AAAATACATGA-CTTTAACG
1 AAAATACATGATCTTTAACG
*
73919 AAAATACATGCTCTT
1 AAAATACATGATCTT
73934 GGCCGAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (20 bp):
AAAATACATGATCTTTAACG
Found at i:75459 original size:36 final size:36
Alignment explanation
Indices: 75412--75516 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
75402 GATACAATCT
75412 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
75448 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
75484 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
75517 ACTTTGATGT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:75474 original size:11 final size:11
Alignment explanation
Indices: 75415--75499 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
75405 ACAATCTGTC
75415 CATCACCATTAT
1 CATCACCA-TAT
*
75427 CA-CGCCTATAT
1 CATCACC-ATAT
75438 CATCACCATAGT
1 CATCACCATA-T
75450 CCATCACCATTAT
1 -CATCACCA-TAT
75463 CA-CACCTATAT
1 CATCACC-ATAT
75474 CATCACCATATT
1 CATCACCATA-T
75486 CCATCACCATAT
1 -CATCACCATAT
75498 CA
1 CA
75500 CGCCTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:75859 original size:33 final size:33
Alignment explanation
Indices: 75817--75885 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
75807 GTTGATGAAT
*
75817 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
75850 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
75883 GAA
1 GAA
75886 TATGGTGATG
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:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:75926 original size:36 final size:36
Alignment explanation
Indices: 75867--75968 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
75857 GATGTTATTG
75867 GCGTGAT-ATGGTGATGGAATATGGTGATGATATAA
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
75902 GCGTGATAATGGTGATGGACTATGGTGATGATATAG
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
75938 GCGTGATAATGGAGATGGATTATGGTGATGA
1 GCGTGATAATGGTGATGGAATATGGTGATGA
75969 AAATAGTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 7 0.11
36 55 0.89
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
GCGTGATAATGGTGATGGAATATGGTGATGATATAA
Found at i:81549 original size:33 final size:33
Alignment explanation
Indices: 81507--81575 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
81497 GTTGATGAAT
*
81507 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
81540 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
81573 GAA
1 GAA
81576 TATGGTGATG
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:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:81616 original size:36 final size:36
Alignment explanation
Indices: 81557--81658 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
81547 GATGTTATTG
81557 GCGTGAT-ATGGTGATGGAATATGGTGATGATATAA
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
81592 GCGTGATAATGGTGATGGACTATGGTGATGATATAG
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
81628 GCGTGATAATGGAGATGGATTATGGTGATGA
1 GCGTGATAATGGTGATGGAATATGGTGATGA
81659 AAATAGTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 7 0.11
36 55 0.89
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
GCGTGATAATGGTGATGGAATATGGTGATGATATAA
Found at i:89736 original size:20 final size:21
Alignment explanation
Indices: 89695--89743 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
89685 GTAAAGCTAT
*
89695 TGAGCTAATATAAACATAACA
1 TGAGCTAAAATAAACATAACA
*
89716 TGAGCTAAAAT-AACATGACA
1 TGAGCTAAAATAAACATAACA
89736 TGAGCTAA
1 TGAGCTAA
89744 TGAATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAATAAACATAACA
Found at i:90364 original size:17 final size:17
Alignment explanation
Indices: 90323--90365 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
90313 ATTTAAACAT
* *
90323 GTAGTTCATTTAGCTAT
1 GTAGTTCATTTAACTAA
* *
90340 GCACTTCATTTAACTAA
1 GTAGTTCATTTAACTAA
90357 GTAGTTCAT
1 GTAGTTCAT
90366 CGATTAAACT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (17 bp):
GTAGTTCATTTAACTAA
Found at i:90378 original size:17 final size:16
Alignment explanation
Indices: 90358--90423 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
90348 TTTAACTAAG
90358 TAGTTCATCGATTAAAC
1 TAGTTCATC-ATTAAAC
*
90375 TAG-T--TCATTGAAC
1 TAGTTCATCATTAAAC
*
90388 TAGTTCATTCATCAAAC
1 TAGTTCA-TCATTAAAC
*
90405 TAGTTCATTTATTAAAC
1 TAGTTCA-TCATTAAAC
90422 TA
1 TA
90424 ACTCTTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
13 9 0.22
14 3 0.08
16 1 0.03
17 27 0.68
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (16 bp):
TAGTTCATCATTAAAC
Found at i:90390 original size:13 final size:13
Alignment explanation
Indices: 90372--90396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90362 TCATCGATTA
90372 AACTAGTTCATTG
1 AACTAGTTCATTG
90385 AACTAGTTCATT
1 AACTAGTTCATT
90397 CATCAAACTA
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:0.12, T:0.40
Consensus pattern (13 bp):
AACTAGTTCATTG
Found at i:118553 original size:15 final size:15
Alignment explanation
Indices: 118518--118546 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
118508 GTGCTTCAAC
118518 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
118532 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
118547 CTTTTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:118569 original size:27 final size:28
Alignment explanation
Indices: 118539--118600 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
118529 CTTTTCTTTG
** *
118539 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTCGGAATGCTTCAATTT
* *
118566 CTTTTTTTCTTTCGGAGTGCTTCAATTT
1 CTTTTCTTCTTTCGGAATGCTTCAATTT
118594 CTTTTCT
1 CTTTTCT
118601 GATTTTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTCGGAATGCTTCAATTT
Found at i:121141 original size:13 final size:12
Alignment explanation
Indices: 121123--121164 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
121113 GCTTACTTTC
121123 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
121136 TCTTTTT-CTTT
1 TCTTTTTGATTT
121147 TCTTTTCTGATTT
1 TCTTTT-TGATTT
121160 TCTTT
1 TCTTT
121165 CTTTTTGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:121151 original size:24 final size:25
Alignment explanation
Indices: 121118--121164 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
121108 CCTTGGCTTA
121118 CTTTCTCTTTT-TGAATTTTCTTTTT
1 CTTTCTCTTTTCTG-ATTTTCTTTTT
121143 CTTT-TCTTTTCTGATTTTCTTT
1 CTTTCTCTTTTCTGATTTTCTTT
121165 CTTTTTGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.72
Consensus pattern (25 bp):
CTTTCTCTTTTCTGATTTTCTTTTT
Found at i:121952 original size:19 final size:20
Alignment explanation
Indices: 121911--121961 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
121901 GAAACCCCTT
*
121911 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
121931 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
121950 TGAAGATACATG
1 TGAAAATACATG
121962 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:122837 original size:13 final size:13
Alignment explanation
Indices: 122819--122844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122809 GTTATAGGCG
122819 TGAAAATGGTGAT
1 TGAAAATGGTGAT
122832 TGAAAATGGTGAT
1 TGAAAATGGTGAT
122845 GAACAGATAG
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:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAATGGTGAT
Found at i:123231 original size:19 final size:20
Alignment explanation
Indices: 123189--123231 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
123179 GAAACCCCTT
*
123189 TGAAAACACATGATTTTAAA
1 TGAAAACACATAATTTTAAA
*
123209 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTAAA
123228 TGAA
1 TGAA
123232 GATAAAGGCT
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:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTAAA
Found at i:125261 original size:16 final size:16
Alignment explanation
Indices: 125240--125272 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
125230 TTCTGCCACC
125240 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
125256 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
125272 T
1 T
125273 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:129976 original size:16 final size:16
Alignment explanation
Indices: 129955--129987 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
129945 TTCTGCCACC
*
129955 TATGTTAGAATGCAAA
1 TATGTTAGAATACAAA
129971 TATGTTAGAATACAAA
1 TATGTTAGAATACAAA
129987 T
1 T
129988 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATACAAA
Found at i:134393 original size:11 final size:11
Alignment explanation
Indices: 134377--134407 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
134367 GTGGAATATG
134377 GTAAATAAACA
1 GTAAATAAACA
134388 GTAAATAAACA
1 GTAAATAAACA
*
134399 GCAAATAAA
1 GTAAATAAA
134408 ATGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:138185 original size:18 final size:17
Alignment explanation
Indices: 138164--138213 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
138154 TTGAAATTTC
138164 TTTTTTCTTTTCTGAATT
1 TTTTTTCTTTT-TGAATT
**
138182 TTTTATTCTTTTTGTCTT
1 TTTT-TTCTTTTTGAATT
138200 TTTCTTTCTTTTTG
1 TTT-TTTCTTTTTG
138214 CACTCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTGAATT
Found at i:146396 original size:33 final size:33
Alignment explanation
Indices: 146356--146424 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
146346 TATTACAATC
146356 ATCATATGATTGGTCTTTGGGCATACTCTAACA
1 ATCATATGATTGGTCTTTGGGCATACTCTAACA
*
146389 ATCATATGATTGGTCTTTGGGCATACTTTAACA
1 ATCATATGATTGGTCTTTGGGCATACTCTAACA
146422 ATC
1 ATC
146425 TCCCACTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (33 bp):
ATCATATGATTGGTCTTTGGGCATACTCTAACA
Found at i:151264 original size:22 final size:23
Alignment explanation
Indices: 151237--151310 Score: 107
Period size: 22 Copynumber: 3.3 Consensus size: 23
151227 AAAATCAGCA
*
151237 AAGAAA-TTGAAGCACTCAAAAG
1 AAGAAATTTCAAGCACTCAAAAG
151259 AAGAAAATTTCAAGCACTCAAAA-
1 AAG-AAATTTCAAGCACTCAAAAG
*
151282 AAAAAATTTCAAGCACTCAAAAG
1 AAGAAATTTCAAGCACTCAAAAG
151305 AAGAAA
1 AAGAAA
151311 AAGAAAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 22 0.48
23 10 0.22
24 14 0.30
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (23 bp):
AAGAAATTTCAAGCACTCAAAAG
Found at i:151275 original size:24 final size:24
Alignment explanation
Indices: 151246--151311 Score: 118
Period size: 22 Copynumber: 2.8 Consensus size: 24
151236 AAAGAAATTG
151246 AAGCACTCAAAAGAAGAAAATTTC
1 AAGCACTCAAAAGAAGAAAATTTC
151270 AAGCACTCAAAA-AA-AAAATTTC
1 AAGCACTCAAAAGAAGAAAATTTC
151292 AAGCACTCAAAAGAAGAAAA
1 AAGCACTCAAAAGAAGAAAA
151312 AGAAAAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.50
23 4 0.10
24 16 0.40
ACGTcount: A:0.59, C:0.17, G:0.11, T:0.14
Consensus pattern (24 bp):
AAGCACTCAAAAGAAGAAAATTTC
Found at i:151319 original size:14 final size:14
Alignment explanation
Indices: 151300--151332 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
151290 TCAAGCACTC
151300 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
151314 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
151328 AAAAG
1 AAAAG
151333 TTGAAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:153052 original size:11 final size:11
Alignment explanation
Indices: 153038--153062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
153028 TCTGATTTCT
153038 TTCACTTGCAC
1 TTCACTTGCAC
153049 TTCACTTGCAC
1 TTCACTTGCAC
153060 TTC
1 TTC
153063 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:159189 original size:19 final size:19
Alignment explanation
Indices: 159162--159198 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
159152 ACATGATTTT
*
159162 TTTTGATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
159181 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
159199 CTCTTGGCCG
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:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:170879 original size:19 final size:20
Alignment explanation
Indices: 170841--170891 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
170831 GAAACCCCTT
170841 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
170861 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
* *
170880 TTAAGATACATG
1 TGAAAATACATG
170892 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:179964 original size:24 final size:21
Alignment explanation
Indices: 179929--179971 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
179919 GGCTCATTCT
*
179929 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
179952 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
179972 ATCTTGTGGA
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:181214 original size:15 final size:15
Alignment explanation
Indices: 181179--181207 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
181169 GTGCTTCAAC
181179 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
181193 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
181208 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:181257 original size:25 final size:25
Alignment explanation
Indices: 181206--181259 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
181196 TTTGCTTTTC
* * * *
181206 TTCTTTTTGAGTGCTGGATTTTTTT
1 TTCTTTTAGAGTGCTGCAATTTCTT
*
181231 TTCTTTTAGAGTGCTTCAATTTCTT
1 TTCTTTTAGAGTGCTGCAATTTCTT
181256 TTCT
1 TTCT
181260 GATTTTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.61
Consensus pattern (25 bp):
TTCTTTTAGAGTGCTGCAATTTCTT
Found at i:182596 original size:13 final size:12
Alignment explanation
Indices: 182577--182662 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
182567 ATATAGGCGT
182577 GATATGGTGATG
1 GATATGGTGATG
182589 GAATATGGTGAT-
1 G-ATATGGTGATG
*
182601 GATATAGGCG-T-
1 GATAT-GGTGATG
182612 GATAATGGTGATG
1 GAT-ATGGTGATG
182625 GACTATGGTGAT-
1 GA-TATGGTGATG
*
182637 GATATAGG-CAT-
1 GATAT-GGTGATG
182648 GATAATGGTGATG
1 GAT-ATGGTGATG
182661 GA
1 GA
182663 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:182632 original size:36 final size:36
Alignment explanation
Indices: 182559--182663 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
182549 ATTTATAAGT
* *
182559 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
182594 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
182630 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
182664 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:194191 original size:13 final size:12
Alignment explanation
Indices: 194172--194257 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
194162 ATATAGGCGT
194172 GATATGGTGATG
1 GATATGGTGATG
194184 GAATATGGTGAT-
1 G-ATATGGTGATG
*
194196 GATATAGGCG-T-
1 GATAT-GGTGATG
194207 GATAATGGTGATG
1 GAT-ATGGTGATG
194220 GACTATGGTGAT-
1 GA-TATGGTGATG
*
194232 GATATAGGCG-T-
1 GATAT-GGTGATG
194243 GATAATGGTGATG
1 GAT-ATGGTGATG
194256 GA
1 GA
194258 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:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:194227 original size:36 final size:36
Alignment explanation
Indices: 194154--194258 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
194144 ATTTATAAGT
* *
194154 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
194189 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
194225 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
194259 AGATTGTATC
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:216836 original size:15 final size:17
Alignment explanation
Indices: 216800--216833 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
216790 TTTGATAACA
216800 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
216816 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
216832 TT
1 TT
216834 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:219281 original size:19 final size:20
Alignment explanation
Indices: 219247--219285 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
219237 TACATAAAAA
219247 ATACATGATTTTTTAATGAAG
1 ATACATGA-TTTTTAATGAAG
219268 ATACATGA-TTTTAATGAA
1 ATACATGATTTTTAATGAA
219286 AGTACATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
ATACATGATTTTTAATGAAG
Found at i:219298 original size:19 final size:19
Alignment explanation
Indices: 219257--219298 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
219247 ATACATGATT
*
219257 TTTTAATGAAGATACATGA
1 TTTTAATGAAGATACATCA
*
219276 TTTTAATGAA-AGTACATCC
1 TTTTAATGAAGA-TACATCA
219295 TTTT
1 TTTT
219299 GTCCAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (19 bp):
TTTTAATGAAGATACATCA
Found at i:219585 original size:16 final size:16
Alignment explanation
Indices: 219564--219605 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
219554 TGCCTAGAGA
219564 TGAACTAGGTTCAAGG
1 TGAACTAGGTTCAAGG
219580 TGAACTAGGTTCAAGG
1 TGAACTAGGTTCAAGG
*
219596 TGAGCTAGGT
1 TGAACTAGGT
219606 GAGTGTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (16 bp):
TGAACTAGGTTCAAGG
Found at i:220836 original size:19 final size:20
Alignment explanation
Indices: 220802--220845 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
220792 TAAAGGGAAT
220802 AATAATAAGTAATGAAAAGA
1 AATAATAAGTAATGAAAAGA
*
220822 AATAATAAG-AATGAAATGA
1 AATAATAAGTAATGAAAAGA
220841 AATAA
1 AATAA
220846 AGAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (20 bp):
AATAATAAGTAATGAAAAGA
Found at i:221306 original size:19 final size:21
Alignment explanation
Indices: 221256--221307 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
221246 GAAATCCCTT
221256 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
221277 AGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
221296 TGAAGATACATG
1 TGAAAATACATG
221308 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:224720 original size:19 final size:18
Alignment explanation
Indices: 224681--224747 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
224671 TTTCCTTGGC
224681 TTTCTTTCTCTTTTGAAT
1 TTTCTTTCTCTTTTGAAT
* *
224699 TTTCTTTTTCTTTTATAAT
1 TTTCTTTCTCTTTT-GAAT
**
224718 TTTCTTTCT-TTTTGTCT
1 TTTCTTTCTCTTTTGAAT
224735 TTTCTTT-TCTTTT
1 TTTCTTTCTCTTTT
224748 TGCACTCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
16 1 0.02
17 12 0.29
18 17 0.41
19 11 0.27
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTCTTTCTCTTTTGAAT
Found at i:225046 original size:19 final size:20
Alignment explanation
Indices: 225018--225057 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
225008 GAATTATAAT
225018 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
225038 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
225057 A
1 A
225058 AGAAATGATA
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:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:230273 original size:17 final size:16
Alignment explanation
Indices: 230251--230313 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 16
230241 AAATTGGGGT
230251 ACAAAAAGAAAGAAAAG
1 ACAAAAAG-AAGAAAAG
230268 ACAAAAAGAAGAAAA-
1 ACAAAAAGAAGAAAAG
230283 ATTCAGAAAAGAAGAAAAG
1 A--CA-AAAAGAAGAAAAG
230302 --AAAAAGAAGAAA
1 ACAAAAAGAAGAAA
230314 TTCAAAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.26
15 2 0.05
16 7 0.17
17 10 0.24
18 12 0.29
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (16 bp):
ACAAAAAGAAGAAAAG
Found at i:230282 original size:26 final size:25
Alignment explanation
Indices: 230253--230313 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
230243 ATTGGGGTAC
230253 AAAAAGAAAGAAAAGACA-AAAAGAA
1 AAAAAGAAAGAAAAGA-AGAAAAGAA
***
230278 GAAAAATTCAGAAAAGAAGAAAAGAA
1 -AAAAAGAAAGAAAAGAAGAAAAGAA
230304 AAAGAAGAAA
1 AAA-AAGAAA
230314 TTCAAAAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAAAGAAAGAAAAGAAGAAAAGAA
Found at i:231053 original size:24 final size:24
Alignment explanation
Indices: 231026--231078 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
231016 TCAAAACATC
*
231026 AAGAGATATGTCTTGT-GAATCACA
1 AAGAGACATGTCTTGTAG-ATCACA
*
231050 AAGAGACATGTCTTGTAGATCACG
1 AAGAGACATGTCTTGTAGATCACA
231074 AAGAG
1 AAGAG
231079 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (24 bp):
AAGAGACATGTCTTGTAGATCACA
Found at i:231872 original size:29 final size:30
Alignment explanation
Indices: 231840--231898 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
231830 CTTAGCTTTA
**
231840 TATTATGTTTACATATGTTTTAGAT-TCAT
1 TATTATGTTTACATATCATTTAGATATCAT
*
231869 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
231899 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTATGTTTACATATCATTTAGATATCAT
Found at i:232796 original size:19 final size:21
Alignment explanation
Indices: 232772--232823 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
232762 CGGCCAAGAG
*
232772 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
232791 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
232812 CATGTATTTTCA
1 CATGTATTTTCA
232824 AAGGGGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:233192 original size:13 final size:13
Alignment explanation
Indices: 233174--233218 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
233164 CATTGCCATT
*
233174 TCATCATCATCCA
1 TCATCAACATCCA
*
233187 TCATCAACATCCT
1 TCATCAACATCCA
*
233200 TCATCAAGA-CCA
1 TCATCAACATCCA
233212 TCATCAA
1 TCATCAA
233219 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:234589 original size:15 final size:14
Alignment explanation
Indices: 234545--234592 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
234535 TTGGAAATAA
234545 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
234559 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
234576 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
234591 GA
1 GA
234593 TATCAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:234589 original size:26 final size:24
Alignment explanation
Indices: 234541--234594 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 24
234531 TTAATTGGAA
234541 ATAAGAAATGAAAGAAATGGAAATTG
1 ATAAGAAATGAAAGAAA-GGAAA-TG
234567 ATAAGAAATGAAATGGAAA-GAAATG
1 ATAAGAAATGAAA--GAAAGGAAATG
234592 ATA
1 ATA
234595 TCAAGGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (24 bp):
ATAAGAAATGAAAGAAAGGAAATG
Found at i:239783 original size:24 final size:21
Alignment explanation
Indices: 239749--239791 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
239739 TCCACAAGAT
*
239749 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
239771 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
239792 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:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:245355 original size:24 final size:21
Alignment explanation
Indices: 245320--245362 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
245310 GGCTCATTCT
*
245320 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
245343 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
245363 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:246538 original size:15 final size:15
Alignment explanation
Indices: 246502--246531 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
246492 TGTGCTTCAA
246502 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
246516 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
246531 T
1 T
246532 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:251342 original size:13 final size:14
Alignment explanation
Indices: 251310--251348 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
251300 AATACTATCG
251310 TTCCATCACCATCT
1 TTCCATCACCATCT
251324 TTCCATCACCATC-
1 TTCCATCACCATCT
251337 TTCCATCACCAT
1 TTCCATCACCAT
251349 TGACGGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (14 bp):
TTCCATCACCATCT
Found at i:251806 original size:7 final size:7
Alignment explanation
Indices: 251794--251840 Score: 55
Period size: 6 Copynumber: 7.0 Consensus size: 7
251784 TGGAGTGCAA
251794 AAGAAAG
1 AAGAAAG
251801 AAGAAAG
1 AAGAAAG
251808 AAGAAA-
1 AAGAAAG
251814 AAGAAA-
1 AAGAAAG
251820 AAGAAA-
1 AAGAAAG
*
251826 AAAAAATG
1 AAGAAA-G
251834 AAGAAAG
1 AAGAAAG
251841 TTGCAAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 17 0.47
7 14 0.39
8 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (7 bp):
AAGAAAG
Done.