Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_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: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 21
Found at i:315 original size:12 final size:12
Alignment explanation
Indices: 298--324 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
288 ACTGATTTCT
298 TTTTATATCTCC
1 TTTTATATCTCC
310 TTTTATATCTCC
1 TTTTATATCTCC
322 TTT
1 TTT
325 CTTGTTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTATATCTCC
Found at i:1806 original size:35 final size:36
Alignment explanation
Indices: 1737--1816 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
1727 TACAATCTGT
**
1737 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
1773 TCATCACCATAGTCCATCCCCA-TATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
1808 TCATTACCA
1 TCATCACCA
1817 AATTCCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 21 0.52
36 19 0.47
ACGTcount: A:0.29, C:0.39, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:2229 original size:21 final size:21
Alignment explanation
Indices: 2187--2224 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2177 GTGCTACAAC
2187 AAAAAACAACAAGAAAGAAGA
1 AAAAAACAACAAGAAAGAAGA
2208 AAAAAACAA-AA-AAAGAA
1 AAAAAACAACAAGAAAGAA
2225 AAGAATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAACAACAAGAAAGAAGA
Found at i:2533 original size:17 final size:17
Alignment explanation
Indices: 2511--2543 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2501 ATCCTACCCT
2511 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
2528 TATACCCTAACCATTT
1 TATACCATAACCATTT
2544 TTTAAGCCGA
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:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:6220 original size:22 final size:24
Alignment explanation
Indices: 6176--6222 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
6166 TATCACGCCT
6176 ATATCATCGCCATAGTCCATCACC
1 ATATCATCGCCATAGTCCATCACC
6200 ATATCA-CGCCTATA-T-CATCACC
1 ATATCATCGCC-ATAGTCCATCACC
6222 A
1 A
6223 AATTCCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.32, C:0.36, G:0.06, T:0.26
Consensus pattern (24 bp):
ATATCATCGCCATAGTCCATCACC
Found at i:6230 original size:35 final size:36
Alignment explanation
Indices: 6143--6230 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 36
6133 TACAATCTGT
*
6143 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
* *
6179 TCATCGCCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
6214 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
6231 TTCCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 27 0.59
36 19 0.41
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.28
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:9026 original size:24 final size:21
Alignment explanation
Indices: 8991--9033 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
8981 GGCTCATTCT
*
8991 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
9014 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
9034 ATCTTGTACA
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:18955 original size:16 final size:16
Alignment explanation
Indices: 18934--18966 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18924 GAGAAAAGTT
*
18934 AGAAAATCAGAAAAGA
1 AGAAAATAAGAAAAGA
18950 AGAAAATAAGAAAAGA
1 AGAAAATAAGAAAAGA
18966 A
1 A
18967 AAGAAAAAGA
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:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (16 bp):
AGAAAATAAGAAAAGA
Found at i:22557 original size:18 final size:18
Alignment explanation
Indices: 22507--22549 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
22497 TTGGGGTGCA
*
22507 AAAAGAAGAAAA-AATCAG
1 AAAAGAAGAAAAGAA-AAG
22525 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
22543 AAAAGAA
1 AAAAGAA
22550 AAAGAGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:29468 original size:19 final size:20
Alignment explanation
Indices: 29444--29483 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
29434 TATCCTTTCT
29444 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
29463 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
29483 T
1 T
29484 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:57160 original size:13 final size:13
Alignment explanation
Indices: 57138--57167 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57128 ACTAAACACC
57138 TTTC-ACATACCT
1 TTTCAACATACCT
57150 TTTCAACATACCT
1 TTTCAACATACCT
57163 TTTCA
1 TTTCA
57168 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:59944 original size:20 final size:20
Alignment explanation
Indices: 59903--59946 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59893 GTGCTTCCAA
**
59903 CTTTTTCTTTCTTTTCTTTG
1 CTTTTTCTTTCTTTTCAGTG
59923 CTTTTTC-TTCTTTTTCAGTG
1 CTTTTTCTTTC-TTTTCAGTG
59943 CTTT
1 CTTT
59947 GACTTTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.70
Consensus pattern (20 bp):
CTTTTTCTTTCTTTTCAGTG
Found at i:65332 original size:13 final size:12
Alignment explanation
Indices: 65314--65343 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
65304 TGGCCAAAGA
65314 TGAAAAGGTATG
1 TGAAAAGGTATG
65326 TTGAAAAGGTATG
1 -TGAAAAGGTATG
65339 TGAAA
1 TGAAA
65344 GATGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Found at i:66600 original size:20 final size:20
Alignment explanation
Indices: 66575--66621 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
66565 ATTTATGTTA
66575 TTAGCTCATATGTATTCATT
1 TTAGCTCATATGTATTCATT
66595 TTAGCTCATATGTATTCATT
1 TTAGCTCATATGTATTCATT
66615 TTAGCTC
1 TTAGCTC
66622 TTAGGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (20 bp):
TTAGCTCATATGTATTCATT
Found at i:67211 original size:63 final size:63
Alignment explanation
Indices: 67135--67260 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
67125 TCCTATGCAT
67135 AAGGCTGCACCATAAGGCTCCCTAGAACACCCATGTGCGTGTCAAATGACCAGCCACCATGTG
1 AAGGCTGCACCATAAGGCTCCCTAGAACACCCATGTGCGTGTCAAATGACCAGCCACCATGTG
*
67198 AAGGCTGCACCATAAGGCTCCCTAGAACACCCATGTGCGTGTCATATGACCAGCCACCATGTG
1 AAGGCTGCACCATAAGGCTCCCTAGAACACCCATGTGCGTGTCAAATGACCAGCCACCATGTG
67261 CCTTCTCATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (63 bp):
AAGGCTGCACCATAAGGCTCCCTAGAACACCCATGTGCGTGTCAAATGACCAGCCACCATGTG
Found at i:70844 original size:13 final size:12
Alignment explanation
Indices: 70826--70855 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
70816 TAGCCAAAGA
70826 TGAAAAGGTATG
1 TGAAAAGGTATG
70838 TTGAAAAGGTATG
1 -TGAAAAGGTATG
70851 TGAAA
1 TGAAA
70856 CATGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Found at i:78597 original size:24 final size:24
Alignment explanation
Indices: 78547--78600 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
78537 TTGCTTTTTC
* *
78547 TTCTTTTTTTTAAGTGCTTGAATT
1 TTCTTTCTTTTAAGTGCTTCAATT
*
78571 TTCTTTCTTTTAGAGTGCTTCTA-T
1 TTCTTTCTTTTA-AGTGCTTCAATT
78595 TTCTTT
1 TTCTTT
78601 TTTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (24 bp):
TTCTTTCTTTTAAGTGCTTCAATT
Found at i:85728 original size:16 final size:16
Alignment explanation
Indices: 85709--85774 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
85699 AGTTATTATC
85709 ATAATA-AACTATAGAT
1 ATAATATAA-TATAGAT
*
85725 ATAATATAATATATAT
1 ATAATATAATATAGAT
85741 AT-ATAT-ATATATGAT
1 ATAATATAATATA-GAT
*
85756 AATAATTATATTATA-AT
1 -ATAA-TATAATATAGAT
85773 AT
1 AT
85775 TTATGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 5 0.12
15 6 0.15
16 18 0.44
17 5 0.12
18 3 0.07
19 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAATATAATATAGAT
Found at i:90308 original size:9 final size:9
Alignment explanation
Indices: 90296--90344 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 9
90286 TCTTTTTGAA
90296 TTTCTTTTT
1 TTTCTTTTT
90305 TTTCTTTTTTT
1 TTTC--TTTTT
90316 TTTCTTCTTT
1 TTTCTT-TTT
*
90326 TTGTCTTTTC
1 TT-TCTTTTT
90336 TTTCTTTTT
1 TTTCTTTTT
90345 GTACTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 12 0.35
10 9 0.26
11 13 0.38
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:90319 original size:20 final size:20
Alignment explanation
Indices: 90296--90344 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
90286 TCTTTTTGAA
* *
90296 TTTCTTTTTTTTCTTTTTTT
1 TTTCTTTTTTTTCTCTTTTC
* *
90316 TTTCTTCTTTTTGTCTTTTC
1 TTTCTTTTTTTTCTCTTTTC
90336 TTTCTTTTT
1 TTTCTTTTT
90345 GTACTCCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTTTTCTCTTTTC
Found at i:90670 original size:22 final size:21
Alignment explanation
Indices: 90644--90684 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
90634 GGCTACATAA
90644 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
90666 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
90685 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:96959 original size:22 final size:25
Alignment explanation
Indices: 96910--96963 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
96900 TTTCTTTTTT
96910 TTTCTTCCTCTTTGAGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
96935 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
96958 TTTCTT
1 TTTCTT
96964 TTCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:96972 original size:13 final size:14
Alignment explanation
Indices: 96953--96992 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
96943 TTTGAGTGCT
96953 TTGATTTTCTTTTC
1 TTGATTTTCTTTTC
96967 -TGATTTT-TTTTC
1 TTGATTTTCTTTTC
*
96979 TTGCTTTTCTTTTC
1 TTGATTTTCTTTTC
96993 ACTTCTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 13 0.57
14 5 0.22
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (14 bp):
TTGATTTTCTTTTC
Found at i:101623 original size:14 final size:15
Alignment explanation
Indices: 101595--101637 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
101585 TGGCTTTGCT
101595 TTCTTTTTGAATTTC
1 TTCTTTTTGAATTTC
*
101610 TTCTTTTT-ATTTTC
1 TTCTTTTTGAATTTC
101624 TTCTTTTCTGAATT
1 TTCTTTT-TGAATT
101638 GTTTTCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 9 0.38
16 3 0.12
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (15 bp):
TTCTTTTTGAATTTC
Found at i:101659 original size:30 final size:30
Alignment explanation
Indices: 101596--101662 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
101586 GGCTTTGCTT
*
101596 TCTTTT-TGAATTTCTTCTTTTTATTTTCT
1 TCTTTTCTGAATTTCTTCTTTTTATTTTCG
*
101625 TCTTTTCTGAATTGTTTTCTTCTTT-TTTT-G
1 TCTTTTCTGAATT-TCTTCTT-TTTATTTTCG
101655 TCTTTTCT
1 TCTTTTCT
101663 TTCATTTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 6 0.18
30 14 0.42
31 10 0.30
32 3 0.09
ACGTcount: A:0.07, C:0.15, G:0.06, T:0.72
Consensus pattern (30 bp):
TCTTTTCTGAATTTCTTCTTTTTATTTTCG
Found at i:101906 original size:20 final size:21
Alignment explanation
Indices: 101883--101935 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
101873 GATAAGAAAG
101883 GAATATGAATAATAAAG-GAA
1 GAATATGAATAATAAAGAGAA
*
101903 GAATAAATGGAATAATAAAGATAA
1 GAAT--AT-GAATAATAAAGAGAA
101927 GAA-ATGAAT
1 GAATATGAAT
101936 TGAAATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 2 0.07
23 11 0.39
24 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (21 bp):
GAATATGAATAATAAAGAGAA
Found at i:101919 original size:12 final size:11
Alignment explanation
Indices: 101889--101922 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
101879 AAAGGAATAT
101889 GAATAATAAAG
1 GAATAATAAAG
*
101900 GAAGAATAAATG
1 GAATAATAAA-G
101912 GAATAATAAAG
1 GAATAATAAAG
101923 ATAAGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (11 bp):
GAATAATAAAG
Found at i:103869 original size:2 final size:2
Alignment explanation
Indices: 103862--103945 Score: 126
Period size: 2 Copynumber: 45.0 Consensus size: 2
103852 ACTATAGATA
103862 AT AT AT 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
103904 AT AT AT AT AT AT AT AT AT -T AT A- AT A- AT -T AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103940 AT AT AT
1 AT AT AT
103946 GAAATAAGCA
Statistics
Matches: 76, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
1 6 0.08
2 70 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105728 original size:13 final size:12
Alignment explanation
Indices: 105710--105739 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
105700 TAGCCAAAGA
105710 TGAAAAGGTATG
1 TGAAAAGGTATG
105722 TTGAAAAGGTATG
1 -TGAAAAGGTATG
105735 TGAAA
1 TGAAA
105740 CATGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Found at i:108491 original size:25 final size:26
Alignment explanation
Indices: 108440--108497 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
108430 AAATCAGCAA
* * *
108440 AAGAAATTGAAGCACTCCAAAAGAAG
1 AAGAAAATCAAGCACTCCAAAAAAAG
108466 AAGAAAATCAAGCAC-CCAAAAAAAG
1 AAGAAAATCAAGCACTCCAAAAAAAG
108491 AAGAAAA
1 AAGAAAA
108498 GAAAAGAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.62, C:0.16, G:0.16, T:0.07
Consensus pattern (26 bp):
AAGAAAATCAAGCACTCCAAAAAAAG
Found at i:120759 original size:32 final size:32
Alignment explanation
Indices: 120718--120781 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
120708 CTCAAATCAC
120718 CATAATCATACATGGCAGCAAGGCATTTAGCT
1 CATAATCATACATGGCAGCAAGGCATTTAGCT
120750 CATAATCATACATGGCAGCAAGGCATTTAGCT
1 CATAATCATACATGGCAGCAAGGCATTTAGCT
120782 TGGAATGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (32 bp):
CATAATCATACATGGCAGCAAGGCATTTAGCT
Found at i:121704 original size:12 final size:12
Alignment explanation
Indices: 121687--121716 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
121677 AAAAGAAAAA
121687 TGCAAAAAGAAG
1 TGCAAAAAGAAG
*
121699 TGCAAAATGAAG
1 TGCAAAAAGAAG
121711 TGCAAA
1 TGCAAA
121717 GTCAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13
Consensus pattern (12 bp):
TGCAAAAAGAAG
Found at i:121764 original size:24 final size:23
Alignment explanation
Indices: 121750--121792 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
121740 AACGAAAGTG
121750 AAGCACTCAAAAGAAAGAAAATC
1 AAGCACTCAAAAGAAAGAAAATC
*
121773 CAGCACTCAAAAG-AAGAAAA
1 AAGCACTCAAAAGAAAGAAAA
121793 AGCAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.60, C:0.19, G:0.14, T:0.07
Consensus pattern (23 bp):
AAGCACTCAAAAGAAAGAAAATC
Found at i:121796 original size:19 final size:20
Alignment explanation
Indices: 121750--121812 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 20
121740 AACGAAAGTG
121750 AAGCACTCAAAAGAAAGAAA
1 AAGCACTCAAAAGAAAGAAA
121770 ATCCAGCACTCAAAAG-AAGAAA
1 A---AGCACTCAAAAGAAAGAAA
***
121792 AAGCAAAGAAAAGAAAGAAA
1 AAGCACTCAAAAGAAAGAAA
121812 A
1 A
121813 GAAGTTGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.25
20 8 0.22
22 7 0.19
23 12 0.33
ACGTcount: A:0.65, C:0.14, G:0.16, T:0.05
Consensus pattern (20 bp):
AAGCACTCAAAAGAAAGAAA
Found at i:123733 original size:25 final size:25
Alignment explanation
Indices: 123699--123755 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
123689 AAGCATGATG
123699 GACGCAAGGTAACCTTGATGCCTTT
1 GACGCAAGGTAACCTTGATGCCTTT
123724 GACGCAAGGTAACCTTGATGCCTTT
1 GACGCAAGGTAACCTTGATGCCTTT
123749 GACGCAA
1 GACGCAA
123756 AAAGAGGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (25 bp):
GACGCAAGGTAACCTTGATGCCTTT
Found at i:128260 original size:35 final size:36
Alignment explanation
Indices: 128203--128270 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
128193 ATACAATCTG
*
128203 TCCATCACCATTATCATGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
128239 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
128271 ACTTCTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:132315 original size:35 final size:36
Alignment explanation
Indices: 132259--132326 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
132249 ATACAATCTG
132259 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
132295 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
132327 ACTTCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:133792 original size:11 final size:13
Alignment explanation
Indices: 133760--133789 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
133750 TGTCCAAAGA
133760 TGAAAAGGTATGT
1 TGAAAAGGTATGT
133773 TGAAAAGGTATG-
1 TGAAAAGGTATGT
133785 TGAAA
1 TGAAA
133790 GGTGCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:142639 original size:14 final size:15
Alignment explanation
Indices: 142606--142651 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
142596 AATTTGGAGT
142606 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
142621 -AAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
142634 GCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
142651 G
1 G
142652 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
17 8 0.32
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:146666 original size:14 final size:15
Alignment explanation
Indices: 146633--146678 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
146623 AATTTGGAGT
146633 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
146648 -AAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
146661 GCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
146678 G
1 G
146679 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
17 8 0.32
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:153184 original size:24 final size:25
Alignment explanation
Indices: 153149--153203 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
153139 ACTTGGAGCC
*
153149 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
153173 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
153197 TCAAGTG
1 TCAAGTG
153204 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:153845 original size:36 final size:36
Alignment explanation
Indices: 153794--153909 Score: 162
Period size: 36 Copynumber: 3.2 Consensus size: 36
153784 TGGCGTGAAA
** *
153794 GTGATGGACTATGGTGATGTTATAGGCGTGCA-AATG
1 GTGATGGAAGATGGTGATGATATAGGCGTG-ATAATG
*
153830 GTGATGGAAGGTGGTGATGATATAGGCGTGATAATG
1 GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
**
153866 GTGATGGATTATGGTGATGATATAGGCGTGATAATG
1 GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
153902 GTGATGGA
1 GTGATGGA
153910 CATATTGTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 1 0.01
36 71 0.99
ACGTcount: A:0.27, C:0.04, G:0.39, T:0.30
Consensus pattern (36 bp):
GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
Found at i:156999 original size:22 final size:20
Alignment explanation
Indices: 156974--157013 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
156964 ATGTTTGTTT
156974 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
156996 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
157014 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:161275 original size:22 final size:20
Alignment explanation
Indices: 161250--161289 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
161240 ATGTTTGTTT
161250 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
161272 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
161290 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:162210 original size:23 final size:23
Alignment explanation
Indices: 162184--162227 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
162174 TGGTACATAT
*
162184 ATGTACATTCTA-CGTGGCATTAC
1 ATGTACAATCTATC-TGGCATTAC
*
162207 ATGTGCAATCTATCTGGCATT
1 ATGTACAATCTATCTGGCATT
162228 CTATGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (23 bp):
ATGTACAATCTATCTGGCATTAC
Found at i:165622 original size:15 final size:15
Alignment explanation
Indices: 165602--165631 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
165592 TCAAGTTTTA
*
165602 AGTATTTTCAAATAT
1 AGTATTGTCAAATAT
165617 AGTATTGTCAAATAT
1 AGTATTGTCAAATAT
165632 TTGAAAGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
AGTATTGTCAAATAT
Found at i:168385 original size:21 final size:21
Alignment explanation
Indices: 168359--168405 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
168349 CGCCTTAAAT
168359 AAGTGTTTAAACCATTTAGAC
1 AAGTGTTTAAACCATTTAGAC
*
168380 AAGTGTTTCAACCATTTAGAC
1 AAGTGTTTAAACCATTTAGAC
168401 AAGTG
1 AAGTG
168406 ACATTAAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (21 bp):
AAGTGTTTAAACCATTTAGAC
Found at i:181278 original size:47 final size:45
Alignment explanation
Indices: 181184--181309 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
181174 GTAACCATGC
* * *
181184 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
181228 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
181275 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
181310 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:184151 original size:18 final size:18
Alignment explanation
Indices: 184128--184194 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
184118 TATATATTAT
184128 AAGAAGAAGAAAAAACAA
1 AAGAAGAAGAAAAAACAA
184146 AAGAAG-A-AAAAAACAA
1 AAGAAGAAGAAAAAACAA
* * *
184162 TAGAAAAAGAAAATGA-AA
1 AAGAAGAAGAAAA-AACAA
*
184180 ACGAAGAAGAAAAAA
1 AAGAAGAAGAAAAAA
184195 TTGAAAACGA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 13 0.33
17 3 0.08
18 22 0.56
19 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.03
Consensus pattern (18 bp):
AAGAAGAAGAAAAAACAA
Found at i:184187 original size:21 final size:20
Alignment explanation
Indices: 184163--184227 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
184153 AAAAAACAAT
184163 AGAAAAAGAAAATGAAAACG
1 AGAAAAAGAAAATGAAAACG
*
184183 AAGAAGAAA-AAATTGAAAACG
1 -AGAA-AAAGAAAATGAAAACG
*
184204 AG--AAAGAAAA-GAAAAAG
1 AGAAAAAGAAAATGAAAACG
184221 AGAAAAA
1 AGAAAAA
184228 AATGAGAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 11 0.30
18 3 0.08
19 3 0.08
20 2 0.05
21 15 0.41
22 3 0.08
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (20 bp):
AGAAAAAGAAAATGAAAACG
Found at i:184213 original size:33 final size:32
Alignment explanation
Indices: 184144--184227 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 32
184134 AAGAAAAAAC
*
184144 AAAAGAAGAAAAAAACAATAGAAAAAGAAAATG
1 AAAAGAAGAAGAAAA-AATAGAAAAAGAAAATG
* *
184177 AAAACGAAGAAGAAAAAATTGAAAACGAGAAA-G
1 AAAA-GAAGAAGAAAAAATAGAAAAAGA-AAATG
*
184210 AAAAGAAAAAGAGAAAAA
1 AAAAGAAGAAGA-AAAAA
184228 AATGAGAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
32 7 0.16
33 24 0.55
34 13 0.30
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.05
Consensus pattern (32 bp):
AAAAGAAGAAGAAAAAATAGAAAAAGAAAATG
Found at i:184217 original size:17 final size:18
Alignment explanation
Indices: 184167--184232 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 18
184157 AACAATAGAA
184167 AAAGAAAATGAAAACGAAG
1 AAAGAAAATGAAAACG-AG
*
184186 AAGAAAAAATTGAAAACGAG
1 AA-AGAAAA-TGAAAACGAG
*
184206 AAAGAAAA-GAAAAAGAG
1 AAAGAAAATGAAAACGAG
184223 AAA-AAAATGA
1 AAAGAAAATGA
184233 GAGATGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.10
17 13 0.32
19 7 0.17
20 9 0.22
21 8 0.20
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (18 bp):
AAAGAAAATGAAAACGAG
Found at i:188401 original size:47 final size:45
Alignment explanation
Indices: 188307--188432 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
188297 GTAACCATGC
* * *
188307 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
188351 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
188398 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
188433 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:190149 original size:6 final size:6
Alignment explanation
Indices: 190133--190162 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
190123 AACGGAAGAC
190133 TCATAGG TCATGG TCATGG TCATGG TCATG
1 TCAT-GG TCATGG TCATGG TCATGG TCATG
190163 ATACAAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (6 bp):
TCATGG
Found at i:191267 original size:18 final size:18
Alignment explanation
Indices: 191244--191310 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
191234 TATCTATTAT
191244 AAGAAGAAGAAAAAACAA
1 AAGAAGAAGAAAAAACAA
191262 AAGAAG-A-AAAAAACAA
1 AAGAAGAAGAAAAAACAA
* * *
191278 TAGAAAAAGAAAATGA-AA
1 AAGAAGAAGAAAA-AACAA
*
191296 ACGAAGAAGAAAAAA
1 AAGAAGAAGAAAAAA
191311 ATGAAAACGA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 13 0.33
17 3 0.08
18 22 0.56
19 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.03
Consensus pattern (18 bp):
AAGAAGAAGAAAAAACAA
Found at i:191303 original size:21 final size:20
Alignment explanation
Indices: 191279--191343 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 20
191269 AAAAAACAAT
191279 AGAAAAAGAAAATGAAAACG
1 AGAAAAAGAAAATGAAAACG
191299 AAGAAGAAA-AAAATGAAAACG
1 -AGAA-AAAGAAAATGAAAACG
*
191320 AG--AAAGAAAA-GAAAAAG
1 AGAAAAAGAAAATGAAAACG
191337 AGAAAAA
1 AGAAAAA
191344 AATGAGAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 11 0.28
18 4 0.10
19 3 0.08
20 2 0.05
21 16 0.41
22 3 0.08
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (20 bp):
AGAAAAAGAAAATGAAAACG
Found at i:191316 original size:27 final size:25
Alignment explanation
Indices: 191281--191342 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
191271 AAAACAATAG
*
191281 AAAAAGAAAATGA-AAACGAAGAAGAA
1 AAAAAGAAAACGAGAAA-GAA-AAGAA
191307 AAAAATGAAAACGAGAAAGAAAAGAA
1 AAAAA-GAAAACGAGAAAGAAAAGAA
*
191333 AAAGAGAAAA
1 AAAAAGAAAA
191343 AAATGAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 14 0.44
27 10 0.31
28 3 0.09
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.03
Consensus pattern (25 bp):
AAAAAGAAAACGAGAAAGAAAAGAA
Found at i:195514 original size:47 final size:45
Alignment explanation
Indices: 195420--195545 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
195410 GTAACAATGC
* * *
195420 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
195464 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
195511 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
195546 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:197384 original size:2 final size:2
Alignment explanation
Indices: 197377--197450 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
197367 GTTACATGTG
197377 AT AT AT 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
197419 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
197451 GATTTGTTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:200311 original size:24 final size:24
Alignment explanation
Indices: 200265--200311 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
200255 CACTGTTTAT
*
200265 TATATATGATGGTTATCATGAATA
1 TATATATGATGGTTATCACGAATA
* *
200289 TATATATGATGTTTATTACGAAT
1 TATATATGATGGTTATCACGAAT
200312 TTTATTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (24 bp):
TATATATGATGGTTATCACGAATA
Found at i:215650 original size:41 final size:39
Alignment explanation
Indices: 215587--215721 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 39
215577 GTTATTATTA
*
215587 GGTGAGTGTAATAAA-GATGATAATGCCTAAGGTGAGGAT
1 GGTGAGTGAAATAAAGGA-GATAATGCCTAAGGTGAGGAT
*
215626 GGTGAGTGAGAAATAAAGGAGATAATGCCTAAAGTGAGGAT
1 GGTGAGT--GAAATAAAGGAGATAATGCCTAAGGTGAGGAT
* * *
215667 GGTGAGTGTAATAAAGG-CATAATGCATAAGGTGAGGAT
1 GGTGAGTGAAATAAAGGAGATAATGCCTAAGGTGAGGAT
*
215705 GATGAGT-ACAATAAAGG
1 GGTGAGTGA-AATAAAGG
215722 TTACAACTCA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
38 32 0.38
39 16 0.19
41 34 0.40
42 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.33, T:0.22
Consensus pattern (39 bp):
GGTGAGTGAAATAAAGGAGATAATGCCTAAGGTGAGGAT
Found at i:217713 original size:41 final size:42
Alignment explanation
Indices: 217601--217718 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
217591 AAGGTTTCTT
* *
217601 GATGATTAAATCC-TTCGGGTCATC-AGTAAGCCTTTCGAGCAT
1 GATGATT-AATCCTTTCAGGTCATCTA-TAAGCCTTTCGAGCAA
* * * *
217643 GGTGATTAATTCTTTCAGGCCATCTATAAGTCTTTCGAGCAA
1 GATGATTAATCCTTTCAGGTCATCTATAAGCCTTTCGAGCAA
217685 GATGA-TAAGTCCTTT-AGGTCATCTATAAGACCTT
1 GATGATTAA-TCCTTTCAGGTCATCTATAAG-CCTT
217719 CGGGCATGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
41 20 0.32
42 41 0.66
43 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (42 bp):
GATGATTAATCCTTTCAGGTCATCTATAAGCCTTTCGAGCAA
Found at i:224080 original size:13 final size:12
Alignment explanation
Indices: 224065--224095 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
224055 GAAAATAAAA
224065 AAAAACTTAATG
1 AAAAACTTAATG
224077 AAAAACTTAATG
1 AAAAACTTAATG
*
224089 TAAAACT
1 AAAAACT
224096 GATGCCCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (12 bp):
AAAAACTTAATG
Found at i:227403 original size:85 final size:85
Alignment explanation
Indices: 227250--227406 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 85
227240 CCAAAGTTTG
* * ** ** *
227250 AAATGGTCATTTATCTTTTATAATCAAAATGAGAGACATCTTATATGTTGTTAATACACCTTTGT
1 AAATGGTCATTTATCTTTTATAATCAAAATGAGAGACACCATATATGTCATTAATACACAGTTAT
227315 ACATTTTTATGAAAAATGCC
66 ACATTTTTATGAAAAATGCC
* * *
227335 AAATGGTCATTTATCTTTTATAATTAAACTGAGTGACACCATATATGTCATTAATACACAGTTAT
1 AAATGGTCATTTATCTTTTATAATCAAAATGAGAGACACCATATATGTCATTAATACACAGTTAT
227400 ACATTTT
66 ACATTTT
227407 CATTTGTTGC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (85 bp):
AAATGGTCATTTATCTTTTATAATCAAAATGAGAGACACCATATATGTCATTAATACACAGTTAT
ACATTTTTATGAAAAATGCC
Found at i:227455 original size:46 final size:46
Alignment explanation
Indices: 227386--227867 Score: 655
Period size: 46 Copynumber: 10.5 Consensus size: 46
227376 TATATGTCAT
* * * * * *
227386 TAATACACAGTTATACATTTTCATTTGTTGCATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * *
227432 TTATACACTC-TTATGCATTTTCATTTTTGGCATCCTTTCATGCTGA
1 TAATGCAC-CGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
227478 TAATGCACCGTTATGTATTTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
227524 TAATGCACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * *
227570 TAATGCACCGTTATTCATTTTCGTTTATGGCATCCTTTCATTCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
227616 TAATACACCATTATGCATTTTCATTTATGGTATCCTTTCATG-CGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * **
227661 TAATGCACCATTATGCATTTTCATTTATGGTACCCTTTCATGTTGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
227707 TAATGCATCGTTATGCATTTTCATTTATGGCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * *
227753 TAATG-GCCATTATGCATTTTCATTTATGGCATCCTTTCATGCTGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
227798 TAATGCATCGTTATGCATTTACATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
227844 TAATGCACCGTTATGCATTTTCAT
1 TAATGCACCGTTATGCATTTTCAT
227868 CTAACTTGCA
Statistics
Matches: 386, Mismatches: 46, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
45 83 0.22
46 303 0.78
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
Found at i:227726 original size:137 final size:135
Alignment explanation
Indices: 227386--227867 Score: 642
Period size: 137 Copynumber: 3.5 Consensus size: 135
227376 TATATGTCAT
* * * * * * * *
227386 TAATACACAGTTATACATTTTCATTTGTTGCATCCTTTCATGCCAATTATACACTC-TTATGCAT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCAC-CGTTATGCAT
* * * *
227450 TTTCATTTTTGGCATCCTTTCATGCTGATAATGCACCGTTATGTATTTTCATTTATGGCATCCTT
65 TTTCATTTATGGCATCCTTTCATTCT-ATAAT-CACCATTATGCATTTTCATTTATGGCATCCTT
227515 TCATGCCGA
128 TCATG-CGA
* *
227524 TAATGCACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCGTTATTCATT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATT
* *
227589 TTCGTTTATGGCATCCTTTCATTCCTATAATACACCATTATGCATTTTCATTTATGGTATCCTTT
66 TTCATTTATGGCATCCTTTCATT-CTATAAT-CACCATTATGCATTTTCATTTATGGCATCCTTT
227654 CATGCGA
129 CATGCGA
* * * ** *
227661 TAATGCACCATTATGCATTTTCATTTATGGTACCCTTTCATGTTGATAATGCATCGTTATGCATT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATT
* **
227726 TTCATTTATGGCATCCTTTCATGTCGATAATGGCCATTATGCATTTTCATTTATGGCATCCTTTC
66 TTCATTTATGGCATCCTTTCAT-TCTATAATCACCATTATGCATTTTCATTTATGGCATCCTTTC
227791 ATGCTGA
130 ATGC-GA
* *
227798 TAATGCATCGTTATGCATTTACATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATT
227863 TTCAT
66 TTCAT
227868 CTAACTTGCA
Statistics
Matches: 302, Mismatches: 38, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
136 35 0.12
137 152 0.50
138 113 0.37
139 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (135 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATT
TTCATTTATGGCATCCTTTCATTCTATAATCACCATTATGCATTTTCATTTATGGCATCCTTTCA
TGCGA
Found at i:231625 original size:20 final size:21
Alignment explanation
Indices: 231584--231633 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
231574 TATATTATGT
231584 TTTACATATGTTTTAGATTCA
1 TTTACATATGTTTTAGATTCA
*
231605 TTTAC-TATGTTTT-CATATCA
1 TTTACATATGTTTTAGAT-TCA
231625 TTTACATAT
1 TTTACATAT
231634 CATGGCAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTACATATGTTTTAGATTCA
Found at i:232576 original size:19 final size:20
Alignment explanation
Indices: 232549--232596 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
232539 CCAAAAGCAT
*
232549 GTATCTTCATT-AAAATCAC
1 GTATTTTCATTAAAAATCAC
* *
232568 GTGTTTTCATTAAAAATCAT
1 GTATTTTCATTAAAAATCAC
232588 GTATTTTCA
1 GTATTTTCA
232597 AAGGGGTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (20 bp):
GTATTTTCATTAAAAATCAC
Found at i:232977 original size:11 final size:12
Alignment explanation
Indices: 232951--232983 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
232941 ACGCCTATAA
*
232951 CATCATCATATC
1 CATCACCATATC
232963 CATCACCAT-TC
1 CATCACCATATC
232974 CATCACCATA
1 CATCACCATA
232984 AAGCTATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.27
Consensus pattern (12 bp):
CATCACCATATC
Found at i:236404 original size:8 final size:8
Alignment explanation
Indices: 236391--236416 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
236381 CTAGTTCATC
236391 TCTAGGCT
1 TCTAGGCT
236399 TCTAGGCT
1 TCTAGGCT
236407 TCTAGGCT
1 TCTAGGCT
236415 TC
1 TC
236417 CCATGGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (8 bp):
TCTAGGCT
Found at i:236698 original size:19 final size:20
Alignment explanation
Indices: 236674--236724 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
236664 TGGCCAAGAG
*
236674 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
236693 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
236713 CATGTATTTTCA
1 CATGTATTTTCA
236725 AAGGGTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:237121 original size:11 final size:12
Alignment explanation
Indices: 237095--237127 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
237085 ACGCCTACAA
*
237095 CATCATCATATC
1 CATCACCATATC
237107 CATCACCAT-TC
1 CATCACCATATC
237118 CATCACCATA
1 CATCACCATA
237128 AAGCTATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.27
Consensus pattern (12 bp):
CATCACCATATC
Found at i:241120 original size:16 final size:16
Alignment explanation
Indices: 241099--241133 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
241089 TGAAAAAGGT
241099 AAACCAACCTTATTTC
1 AAACCAACCTTATTTC
*
241115 AAACCAAGCTTATTTC
1 AAACCAACCTTATTTC
241131 AAA
1 AAA
241134 GAAATCGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (16 bp):
AAACCAACCTTATTTC
Found at i:243298 original size:14 final size:14
Alignment explanation
Indices: 243279--243309 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
243269 ACTAACCCTA
243279 ATGTTTATTCTGAT
1 ATGTTTATTCTGAT
*
243293 ATGTTTATTCTGCT
1 ATGTTTATTCTGAT
243307 ATG
1 ATG
243310 CATTACGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (14 bp):
ATGTTTATTCTGAT
Found at i:244371 original size:20 final size:20
Alignment explanation
Indices: 244343--244381 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
244333 ATTTTGAGTG
244343 TGTAATATTGATACCCTAGC
1 TGTAATATTGATACCCTAGC
* *
244363 TGTAGTATTGATACTCTAG
1 TGTAATATTGATACCCTAG
244382 GTTAAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTAATATTGATACCCTAGC
Found at i:244544 original size:19 final size:20
Alignment explanation
Indices: 244520--244557 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
244510 TTTGCCCCAA
*
244520 TTCAT-CCACTATCGATACG
1 TTCATCCCAATATCGATACG
244539 TTCATCCCAATATCGATAC
1 TTCATCCCAATATCGATAC
244558 TCTTGCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (20 bp):
TTCATCCCAATATCGATACG
Found at i:245070 original size:25 final size:26
Alignment explanation
Indices: 245028--245076 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
245018 AGGAGGGAGG
*
245028 AAGAGAAAATGAGAAGATAGGAAAATA
1 AAGAAAAAATGAGAAGAT-GGAAAATA
245055 AAGAAAAAAT-AG-AGATGGAAAA
1 AAGAAAAAATGAGAAGATGGAAAA
245077 AATAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 2 0.10
27 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.10
Consensus pattern (26 bp):
AAGAAAAAATGAGAAGATGGAAAATA
Found at i:266837 original size:19 final size:20
Alignment explanation
Indices: 266813--266866 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
266803 TGTAAAAATG
*
266813 GTATCGATACCATAGCA-TA
1 GTATCGATACCATAGAAGTA
*
266832 GTATCGGTACCATAGAATGGTA
1 GTATCGATACCATAGAA--GTA
266854 GTATCGATACCAT
1 GTATCGATACCAT
266867 GGTATGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.52
22 14 0.48
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATAGAAGTA
Found at i:266873 original size:22 final size:22
Alignment explanation
Indices: 266813--266884 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
266803 TGTAAAAATG
*
266813 GTATCGATACCATAGCA---TA
1 GTATCGATACCATAGAATGGTA
*
266832 GTATCGGTACCATAGAATGGTA
1 GTATCGATACCATAGAATGGTA
* *
266854 GTATCGATACCATGGTATGG--
1 GTATCGATACCATAGAATGGTA
266874 GTATCGATACC
1 GTATCGATACC
266885 GAGGGACCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.33
20 11 0.24
22 19 0.42
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (22 bp):
GTATCGATACCATAGAATGGTA
Found at i:267266 original size:54 final size:53
Alignment explanation
Indices: 267208--267374 Score: 210
Period size: 54 Copynumber: 3.1 Consensus size: 53
267198 TTACCAAATA
* * *
267208 GGCACTAATTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTT
* * *
267261 CGGCACTAAGTATGCATTTCACGGAATTCATCATATGTGGATGAATAATCGTTAT
1 -GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT-T
* * *
267316 GACACTAAGTGTACATTTCACGGATTTCATTCC-ATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCA-TCCTATGTGGATGAATAACCG-TTT
267370 GGCAC
1 GGCAC
267375 CATGGGTGCA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
54 92 0.95
55 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (53 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTT
Found at i:267414 original size:108 final size:108
Alignment explanation
Indices: 267210--267406 Score: 243
Period size: 108 Copynumber: 1.8 Consensus size: 108
267200 ACCAAATAGG
* * * *
267210 CACTAATTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACTAAGTATG
1 CACTAAGTGTACATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACCAAGGATG
*** * *
267275 CATTTCACGGAATTCATCATATGTGGATGAATAATCGTTATGA
66 CAAAACACGAAATTCATAATATGTGGATGAATAATCGTTATGA
* * * * * *
267318 CACTAAGTGTACATTTCACGGATTTCATTCC-ATGTGGATGAATAACCGTTTTGGCACCATGGGT
1 CACTAAGTGTACATTTCACGAAATTCA-TCCTATGTGGATGAATAACCATTTCGGCACCAAGGAT
267382 GCAAAACACGAAATTCATAATATGT
65 GCAAAACACGAAATTCATAATATGT
267407 TTATGAATGA
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
108 70 0.96
109 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (108 bp):
CACTAAGTGTACATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACCAAGGATG
CAAAACACGAAATTCATAATATGTGGATGAATAATCGTTATGA
Found at i:267430 original size:108 final size:108
Alignment explanation
Indices: 267208--267430 Score: 234
Period size: 108 Copynumber: 2.1 Consensus size: 108
267198 TTACCAAATA
* * * *
267208 GGCACTAATTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACTAAGTA
1 GGCACTAAGTGTACATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACCAAGGA
*** * * *
267273 TGCATTTCACGGAATTCATCATATGTGGATGAATAATCGTTAT
66 TGCAAAACACGAAATTCATAATATGTGGATGAATAACCGTTAT
* * * * * *
267316 GACACTAAGTGTACATTTCACGGATTTCATTCC-ATGTGGATGAATAACCGTTTTGGCACCATGG
1 GGCACTAAGTGTACATTTCACGAAATTCA-TCCTATGTGGATGAATAACCATTTCGGCACCAAGG
* ** *
267380 GTGCAAAACACGAAATTCATAATATGTTTATGAATGACCGTT-T
65 ATGCAAAACACGAAATTCATAATATGTGGATGAATAACCGTTAT
267423 GGGCACTA
1 -GGCACTA
267431 CTGGTCCATC
Statistics
Matches: 92, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
107 1 0.01
108 88 0.96
109 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (108 bp):
GGCACTAAGTGTACATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACCAAGGA
TGCAAAACACGAAATTCATAATATGTGGATGAATAACCGTTAT
Found at i:273810 original size:54 final size:54
Alignment explanation
Indices: 273719--274091 Score: 496
Period size: 54 Copynumber: 6.9 Consensus size: 54
273709 AAAATAGGCT
* * * * * *
273719 CTAATTGTCCATTTCACAGAATTCATCATATATGGATGAATAATCATTTCGGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
** *
273773 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGCTTCGACA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
* * *
273827 CTAATTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTTGGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
** * *
273881 CTAAGTGTATATTTAACGAAATTCATCCTATGTGGATGAATAACCATTTCGGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
* * *
273935 CTAAGAGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCATTTCAGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
* * ** *
273989 CTATGTGTGCATTTCACGGAATTCATCCTATGTGGAGGAATAACTGTTTCGACA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
* *
274043 CTCAA-TGTGCATTTCACGGAATTCATCCCATATGGATGAATAACCATTT
1 CT-AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTT
274092 TGGCCACATG
Statistics
Matches: 277, Mismatches: 41, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
54 276 1.00
55 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (54 bp):
CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGGCA
Found at i:274230 original size:2 final size:2
Alignment explanation
Indices: 274223--274248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274213 AGAATAATGT
274223 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
274249 ACATTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:275671 original size:21 final size:21
Alignment explanation
Indices: 275645--275685 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
275635 GGTTATGATC
*
275645 GATCCTTTGGACAAACGGATT
1 GATCCTTTGGACAAAAGGATT
*
275666 GATCCTTTGGGCAAAAGGAT
1 GATCCTTTGGACAAAAGGAT
275686 CAATCATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
GATCCTTTGGACAAAAGGATT
Found at i:276867 original size:54 final size:54
Alignment explanation
Indices: 276809--277015 Score: 193
Period size: 54 Copynumber: 3.9 Consensus size: 54
276799 TTCATTGCGA
* * * *
276809 TGCACACGTAGTGCCTATACGGTCATTCATAAACATATTATGAATTCCGTGAGT
1 TGCACACATAGTGCCTAAACGGTTATTCATCAACATATTATGAATTCCGTGAGT
* * * * *
276863 TGCACACATTGTGCCTAAACAGTTGTTCATCAACATATAATGAATTCTGTGAGT
1 TGCACACATAGTGCCTAAACGGTTATTCATCAACATATTATGAATTCCGTGAGT
* * * * * * *
276917 TGTACCCATACTGCCTAAACGATTATTTATCAACATATGATGAATTTCGTGAGT
1 TGCACACATAGTGCCTAAACGGTTATTCATCAACATATTATGAATTCCGTGAGT
* * * * **
276971 TGAACATATAGTGCCCATACGGAAATTCAT-AAC-TCATTATGAATT
1 TGCACACATAGTGCCTAAACGGTTATTCATCAACAT-ATTATGAATT
277016 TCTTAGTTTT
Statistics
Matches: 121, Mismatches: 31, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
52 1 0.01
53 12 0.10
54 108 0.89
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCTAAACGGTTATTCATCAACATATTATGAATTCCGTGAGT
Found at i:283452 original size:23 final size:23
Alignment explanation
Indices: 283422--283487 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
283412 GCTATTTTTT
*
283422 CAAAAAAAAAAACAAAAAAAAGG
1 CAAAAAAAAAAGCAAAAAAAAGG
**
283445 CAAAAAAAAAAGGTAAAAAAAGG
1 CAAAAAAAAAAGCAAAAAAAAGG
*
283468 CACAAAAAAAAGCAAAAAAA
1 CAAAAAAAAAAGCAAAAAAA
283488 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.79, C:0.09, G:0.11, T:0.02
Consensus pattern (23 bp):
CAAAAAAAAAAGCAAAAAAAAGG
Found at i:283462 original size:12 final size:13
Alignment explanation
Indices: 283435--283487 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
283425 AAAAAAAAAC
283435 AAAAAAAAGGCAA
1 AAAAAAAAGGCAA
283448 AAAAAAAAGG---
1 AAAAAAAAGGCAA
* *
283458 TAAAAAAAGGCAC
1 AAAAAAAAGGCAA
283471 AAAAAAAA-GCAA
1 AAAAAAAAGGCAA
283483 AAAAA
1 AAAAA
283488 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 9 0.26
12 8 0.24
13 17 0.50
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGGCAA
Found at i:289287 original size:54 final size:54
Alignment explanation
Indices: 289174--289289 Score: 135
Period size: 54 Copynumber: 2.1 Consensus size: 54
289164 TCATGATATC
* * * * **
289174 ATTCATAAACATATTATGAATTTCGTTGGTTGTACACATAGTGCCTAAACGGTT
1 ATTCATAAACATATGATAAATTCCGTTGGTTGTACACATAGTGCCCAAACGGAA
* * *
289228 GTTCATCAACATATGATAAATTCCG-TGAGTTGTACACATAGTGCCCATACGGAA
1 ATTCATAAACATATGATAAATTCCGTTG-GTTGTACACATAGTGCCCAAACGGAA
289282 ATTCATAA
1 ATTCATAA
289290 CTCATCATGA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (54 bp):
ATTCATAAACATATGATAAATTCCGTTGGTTGTACACATAGTGCCCAAACGGAA
Found at i:289713 original size:19 final size:21
Alignment explanation
Indices: 289660--289713 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
289650 TACCCTTACC
289660 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACTACTATA-T
289682 ATGGTA-CTGATACT-CTAT-T
1 ATGGTATC-GATACTACTATAT
*
289701 ATGGTATCAATAC
1 ATGGTATCGATAC
289714 CATTTCTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 5 0.17
22 12 0.41
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
ATGGTATCGATACTACTATAT
Found at i:291437 original size:19 final size:19
Alignment explanation
Indices: 291413--291459 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
291403 ACTATTCTCT
291413 TTAGCATTTCGAAACTTTC
1 TTAGCATTTCGAAACTTTC
291432 TTAGCATTTCGAAACTTTC
1 TTAGCATTTCGAAACTTTC
*
291451 TTGGCATTT
1 TTAGCATTT
291460 TCCAGTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (19 bp):
TTAGCATTTCGAAACTTTC
Found at i:295691 original size:54 final size:54
Alignment explanation
Indices: 295554--295693 Score: 147
Period size: 54 Copynumber: 2.6 Consensus size: 54
295544 TTCGTTCTGA
* * ** *
295554 TGCACACGTAGTGCCTATACGATCATTCATAAACATATTCTGAATTTCGTTGGT
1 TGCACACATAGTGCCTATACGATAATTCATAAACATATGATGAATTCCGTTGGT
* * * ** *
295608 TGTACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCG-TGAGT
1 TGCACACATAGTGCCTATACGATAATTCATAAACATATGATGAATTCCGTTG-GT
* *
295662 TGCACACATAGTGCCCATACGAAAATTCATAA
1 TGCACACATAGTGCCTATACGATAATTCATAA
295694 CTCATTATGA
Statistics
Matches: 67, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
53 2 0.03
54 65 0.97
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGATAATTCATAAACATATGATGAATTCCGTTGGT
Found at i:296097 original size:22 final size:20
Alignment explanation
Indices: 296065--296120 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
296055 TACCCTTAGC
296065 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACTACTAT--T
*
296087 ATGGTACCGATACT-CTATT
1 ATGGTATCGATACTACTATT
*
296106 ATGGTATCAATACTA
1 ATGGTATCGATACTA
296121 TTTCAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGGTATCGATACTACTATT
Found at i:310435 original size:2 final size:2
Alignment explanation
Indices: 310428--310458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
310418 ATTATTAATA
310428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310459 AGTTTGAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:311389 original size:27 final size:24
Alignment explanation
Indices: 311333--311378 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
311323 AACTGATGTG
311333 ATCATGCCAAGGACCAAACTTCAC
1 ATCATGCCAAGGACCAAACTTCAC
311357 ATCATGCCAAGGACCAAACTTC
1 ATCATGCCAAGGACCAAACTTC
311379 TTCAACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (24 bp):
ATCATGCCAAGGACCAAACTTCAC
Found at i:317266 original size:38 final size:38
Alignment explanation
Indices: 317218--317301 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
317208 TTATTTAAAG
*
317218 AAATATTAATTACAAAAGTA-AATAATAATATCAAAGAATC
1 AAAT-TTAATTA-AAAACTATAATAATAATAT-AAAGAATC
* *
317258 -AATTTAATTAAGAACTATAATCATAATATAAAGAATC
1 AAATTTAATTAAAAACTATAATAATAATATAAAGAATC
317295 AAATTTA
1 AAATTTA
317302 GTAGATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 13 0.33
38 23 0.59
39 3 0.08
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (38 bp):
AAATTTAATTAAAAACTATAATAATAATATAAAGAATC
Found at i:317694 original size:5 final size:5
Alignment explanation
Indices: 317686--317723 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
317676 AATTAAAACA
*
317686 AAAAT AAAA- AAATT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
317724 GATCCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:317698 original size:20 final size:20
Alignment explanation
Indices: 317674--317723 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
317664 TTAAAATATT
317674 TAAATTAAAACAAAAATAAAA
1 TAAATTAAAA-AAAAATAAAA
*
317695 -AAATTAAAATAAAATAAAA
1 TAAATTAAAAAAAAATAAAA
*
317714 TAAAATAAAA
1 TAAATTAAAA
317724 GATCCAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAATTAAAAAAAAATAAAA
Found at i:319427 original size:22 final size:21
Alignment explanation
Indices: 319383--319458 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
319373 TTCAAATAAT
* *
319383 TCGATCGTTATAA-GAAGGGGA
1 TCGATCTTTTTAATGAA-GGGA
*
319404 TCAATCTTTTTAAATGAAGGGA
1 TCGATCTTTTT-AATGAAGGGA
* **
319426 TCGATCATTTTGGTGAAGGGA
1 TCGATCTTTTTAATGAAGGGA
319447 TCGATCCTTTTT
1 TCGAT-CTTTTT
319459 GTAAAGGGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 21 0.48
22 20 0.45
23 3 0.07
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGATCTTTTTAATGAAGGGA
Found at i:319444 original size:21 final size:21
Alignment explanation
Indices: 319418--319469 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
319408 TCTTTTTAAA
319418 TGAAGGGATCGATCATTTTGG
1 TGAAGGGATCGATCATTTTGG
* *
319439 TGAAGGGATCGATCCTTTTTG
1 TGAAGGGATCGATCATTTTGG
*
319460 TAAAGGGATC
1 TGAAGGGATC
319470 AATCCCAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.33
Consensus pattern (21 bp):
TGAAGGGATCGATCATTTTGG
Found at i:323088 original size:39 final size:39
Alignment explanation
Indices: 323034--323112 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
323024 AACCATATTC
323034 TTTGGCTTGCTTGAACCCTTCTTCCTCAATAGTGGACAA
1 TTTGGCTTGCTTGAACCCTTCTTCCTCAATAGTGGACAA
*
323073 TTTGGCTTGCTTGAACCCTTCTTCGTCAATAGTGGACAA
1 TTTGGCTTGCTTGAACCCTTCTTCCTCAATAGTGGACAA
323112 T
1 T
323113 CATATTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (39 bp):
TTTGGCTTGCTTGAACCCTTCTTCCTCAATAGTGGACAA
Found at i:323318 original size:33 final size:33
Alignment explanation
Indices: 323281--323345 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
323271 AAAGTAACTG
323281 AACATGTTAAGAACTTTAACTAGTAAATAACAA
1 AACATGTTAAGAACTTTAACTAGTAAATAACAA
* *
323314 AACATGTTAGGACCTTTAACTAGTAAATAACA
1 AACATGTTAAGAACTTTAACTAGTAAATAACA
323346 TTGGCTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.28
Consensus pattern (33 bp):
AACATGTTAAGAACTTTAACTAGTAAATAACAA
Found at i:325327 original size:13 final size:13
Alignment explanation
Indices: 325309--325334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
325299 ATTAATGGTG
325309 TTAATTTAAAAAT
1 TTAATTTAAAAAT
325322 TTAATTTAAAAAT
1 TTAATTTAAAAAT
325335 AATATAAAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTTAAAAAT
Found at i:327027 original size:28 final size:28
Alignment explanation
Indices: 326985--327047 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
326975 TCTCCTTCGT
* *
326985 TAGGTTTTGTTCCTCAAGATATTTCTTG
1 TAGGTTATGTCCCTCAAGATATTTCTTG
*
327013 TAGGTTATGTCCCTCAAGATTTTTCTTG
1 TAGGTTATGTCCCTCAAGATATTTCTTG
327041 TGAGGTT
1 T-AGGTT
327048 CTAATAAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (28 bp):
TAGGTTATGTCCCTCAAGATATTTCTTG
Found at i:332005 original size:127 final size:126
Alignment explanation
Indices: 331859--332111 Score: 470
Period size: 127 Copynumber: 2.0 Consensus size: 126
331849 TATTTATACT
331859 ACTTAAAGCTTAATTATAACATCTACTCATATTTAATTAAGTTTTAAAAATATAAACCAGTTATA
1 ACTTAAAGCTTAATTATAACATCTACTCATATTTAATTAAGTTTTAAAAATATAAACCAGTTATA
*
331924 GTTAATTTTAACTATTTACATTTAAGCTAATTTCGATGTTATTGTAAAAAGGTTTTACATA
66 GTTAATTTTAACTATTTAAATTTAAGCTAATTTCGATGTTATTGTAAAAAGGTTTTACATA
* *
331985 ACTTAAAAGCTTAATTATAACATCTACTCATATTTAATTAAGTTTTAAAAATATACATCAGTTAT
1 ACTT-AAAGCTTAATTATAACATCTACTCATATTTAATTAAGTTTTAAAAATATAAACCAGTTAT
332050 AGTTAATTTTAACTATTTAAATTTAAGCTAATTTCGATGTTATTGTAAAAAGGTTTTACATA
65 AGTTAATTTTAACTATTTAAATTTAAGCTAATTTCGATGTTATTGTAAAAAGGTTTTACATA
332112 TGGTATGAAC
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
126 4 0.03
127 119 0.97
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (126 bp):
ACTTAAAGCTTAATTATAACATCTACTCATATTTAATTAAGTTTTAAAAATATAAACCAGTTATA
GTTAATTTTAACTATTTAAATTTAAGCTAATTTCGATGTTATTGTAAAAAGGTTTTACATA
Found at i:332590 original size:17 final size:17
Alignment explanation
Indices: 332568--332600 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
332558 TTATCAACAA
*
332568 TATAGTTTATAGTTAAT
1 TATAGTTAATAGTTAAT
332585 TATAGTTAATAGTTAA
1 TATAGTTAATAGTTAA
332601 CATATTAGGT
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:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TATAGTTAATAGTTAAT
Found at i:347113 original size:51 final size:50
Alignment explanation
Indices: 346971--347120 Score: 216
Period size: 49 Copynumber: 3.0 Consensus size: 50
346961 GAATACCATG
346971 AGTGGCACCTTTTATGCC-AAAATGCACTC-TTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAAATGCAC-CGTTATGCATTTAACTTTCATT
* * * *
347020 AGTGGCACCTTTTAGGCCG-AAATGCGCTGTTATGCATTTAACTTTTATT
1 AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
*
347069 AGTGTCACCTTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACC-TTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
347120 A
1 A
347121 TAGAACAGTT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
49 51 0.58
50 9 0.10
51 28 0.32
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (50 bp):
AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:353090 original size:50 final size:50
Alignment explanation
Indices: 353036--353225 Score: 267
Period size: 49 Copynumber: 3.8 Consensus size: 50
353026 GAATACTATG
*
353036 AGTGGCACCTTTTATGCCGAAAATGCGCCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
* * *
353086 AGTGGAACCTTTTATGCCG-AAATACACCGTTATGCATTTAACTTTAATT
1 AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
353135 TGTGGCACCTTTTATGCC-AACATTCACTGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
* * *
353184 AGTGACACCTTTTATGCTGAAATTGCACCGTTATGCATTTAA
1 AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAA
353226 ATAGAGCAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 84 0.69
50 37 0.31
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (50 bp):
AGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:353179 original size:98 final size:100
Alignment explanation
Indices: 353037--353225 Score: 294
Period size: 98 Copynumber: 1.9 Consensus size: 100
353027 AATACTATGA
*
353037 GTGGCACCTTTTATGCCGAAAATGCGCCGTTATGCATTTAACTTTCATTAGTGGA-ACCTTTTAT
1 GTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATTAGT-GACACCTTTTAT
353101 GCCGAAA-TACACCGTTATGCATTTAACTTTAATTT
65 GCCGAAATTACACCGTTATGCATTTAACTTTAATTT
* * *
353136 GTGGCACCTTTTATGCC-AACATTCACTGTTATGCATTTAACTTTCATTAGTGACACCTTTTATG
1 GTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATG
* *
353200 CTGAAATTGCACCGTTATGCATTTAA
66 CCGAAATTACACCGTTATGCATTTAA
353226 ATAGAGCAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
97 2 0.02
98 45 0.55
99 35 0.43
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (100 bp):
GTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATG
CCGAAATTACACCGTTATGCATTTAACTTTAATTT
Found at i:364874 original size:10 final size:10
Alignment explanation
Indices: 364859--364927 Score: 60
Period size: 10 Copynumber: 7.5 Consensus size: 10
364849 TTTTTTTTTC
364859 AAAAAAACAA
1 AAAAAAACAA
364869 AAAAAAAC--
1 AAAAAAACAA
364877 -AAAAAACAA
1 AAAAAAACAA
**
364886 AAAAAGGC--
1 AAAAAAACAA
364894 AAAAAAACAA
1 AAAAAAACAA
**
364904 AAAAAGGC-A
1 AAAAAAACAA
364913 AAAAAAACAA
1 AAAAAAACAA
364923 AAAAA
1 AAAAA
364928 GAGCCAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
7 7 0.16
8 6 0.13
9 7 0.16
10 25 0.56
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:364881 original size:18 final size:18
Alignment explanation
Indices: 364858--364938 Score: 110
Period size: 18 Copynumber: 4.4 Consensus size: 18
364848 ATTTTTTTTT
**
364858 CAAAAAAACAAAAAAAAA
1 CAAAAAAACAAAAAAAGG
364876 C-AAAAAACAAAAAAAGG
1 CAAAAAAACAAAAAAAGG
364893 CAAAAAAACAAAAAAAGG
1 CAAAAAAACAAAAAAAGG
364911 CAAAAAAAACAAAAAAAGAG
1 C-AAAAAAACAAAAAAAG-G
364931 CCAAAAAA
1 -CAAAAAA
364939 GCCAAAATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.26
18 18 0.32
19 16 0.28
20 7 0.12
21 1 0.02
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAGG
Found at i:364939 original size:11 final size:10
Alignment explanation
Indices: 364883--364945 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
364873 AAACAAAAAA
*
364883 CAAAAAAAGG
1 CAAAAAAAGC
364893 CAAAAAAA--
1 CAAAAAAAGC
*
364901 CAAAAAAAGG
1 CAAAAAAAGC
*
364911 CAAAAAAAAC
1 CAAAAAAAGC
*
364921 AAAAAAAGAGC
1 CAAAAAA-AGC
364932 C-AAAAAAGC
1 CAAAAAAAGC
364941 CAAAA
1 CAAAA
364946 TTTCAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 8 0.18
9 4 0.09
10 30 0.68
11 2 0.05
ACGTcount: A:0.75, C:0.14, G:0.11, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:369829 original size:404 final size:409
Alignment explanation
Indices: 369018--369834 Score: 1183
Period size: 404 Copynumber: 2.0 Consensus size: 409
369008 CTTGTGAGGG
369018 AGATTAATCTTCACACTCCAATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATTTA
1 AGATTAATCTTCACACTCCAATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATTTA
* *
369083 TCGTGTTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCTATTTTTCCAC
66 TCGTGTTTACCTTTTCATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCGATTTTTCCAC
*
369148 AAATCCATCCGCACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTTTGATTTCTT
131 AAATCCATCCACACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTTTGATTTCTT
* * * * * * **
369213 TATTATCTTATTTCATCTTTCATTTATTTATCTTTTGTTTATTTTATTCTAATCGTGTTGTCTTG
196 GATTATCTTATTTCATCTTGCATTCATTTATCTTTTGTTAATCTTAGTCT-ATC--GTTACCTTG
* *
369278 ATTCCAGTACATAAAAGAAACCCTAAACAATCCTAGCGACTGCTGCCACCTTCCCATATTCATCA
258 ATTCCAGCACATAAAAGAAACCCTAAACAACCCTAGCGACTGCTGCCACCTTCCCATATTCATCA
*
369343 CATTTGTTCTTCATCGAGTCTAGAGCTTTCTAGGTTTGATTCTTCAATAAGAGCAACGTTCATCA
323 CATTTGTTCTTCATCGAGTCTAGAGCTTTCTAGGTTTGATTCTTCAACAAGAGCAACGTTCATCA
*
369408 ATCCGCCACCGCTTCCCTATCA
388 ACCCGCCACCGCTTCCCTATCA
369430 AGATTAATCTTCACACTCCAATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATT
1 AGATTAATCTTCACACTCCAATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCAT-TT
369495 ATCGTGTTTACCTTTTCATTGCGACTAGGAGGGCTCGATAGGACA-TTATCCATCGA-TTTTCCA
65 ATCGTGTTTACCTTTTCATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCGATTTTTCCA
* * *
369558 CATATCCATCCACACCATCAATCATCTTTACCGTTTACCTTCATAAGGGAGATCTTTTGGTTTCT
130 CAAATCCATCCACACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTTTGATTTCT
* * *
369623 TGGTTATCTTATTTTAT-TTGCAATTCCTTTATCTTGTT-TTAATCTT-GT-T-TC-TTACCTTG
195 TGATTATCTTATTTCATCTTGC-ATTCATTTATCTT-TTGTTAATCTTAGTCTATCGTTACCTTG
* * * * * *
369682 TTTCCAGCACCTAAAAGATACTCT-AAGAACCCTA-CTTG-CTGCCT-CCACCTTCCCCTATTCA
258 ATTCCAGCACATAAAAGAAACCCTAAACAACCCTAGC--GACTG-CTGCCACCTTCCCATATTCA
*
369743 TTCCCCA-TTGTTCTTCATCGAGTCTAGAGCTTTCTAGGTTTGATTCTTCAACAAGAGCAACGTT
320 -T-CACATTTGTTCTTCATCGAGTCTAGAGCTTTCTAGGTTTGATTCTTCAACAAGAGCAACGTT
*
369807 CATTAACCCGCCACCGCTTCCCTATCA
383 CATCAACCCGCCACCGCTTCCCTATCA
369834 A
1 A
369835 TTGGTATCAG
Statistics
Matches: 368, Mismatches: 29, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
402 1 0.00
403 27 0.07
404 111 0.30
405 3 0.01
407 2 0.01
409 1 0.00
410 4 0.01
411 99 0.27
412 74 0.20
413 46 0.12
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (409 bp):
AGATTAATCTTCACACTCCAATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATTTA
TCGTGTTTACCTTTTCATTGCGACTAGGAGGGCTCGATAGGACACTTATCCATCGATTTTTCCAC
AAATCCATCCACACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTTTGATTTCTT
GATTATCTTATTTCATCTTGCATTCATTTATCTTTTGTTAATCTTAGTCTATCGTTACCTTGATT
CCAGCACATAAAAGAAACCCTAAACAACCCTAGCGACTGCTGCCACCTTCCCATATTCATCACAT
TTGTTCTTCATCGAGTCTAGAGCTTTCTAGGTTTGATTCTTCAACAAGAGCAACGTTCATCAACC
CGCCACCGCTTCCCTATCA
Found at i:382920 original size:108 final size:109
Alignment explanation
Indices: 382777--383290 Score: 486
Period size: 108 Copynumber: 4.6 Consensus size: 109
382767 TTTACATACA
* * * * *
382777 TAGTGCCGAAACGGTTATTCATTAACATATGATGAATTCCGTGAATTGCACACTTAGTGCT-TAA
1 TAGTGTCGAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCTCGAA
* *
382841 ACTGTTATTCATCAACATATGATGAATTCCGTGAATTGTACACT
66 ACTGTTATTCATCAACATATGATGAATTACGTGAATTGCACACT
* * *
382885 TAGTATCGAAATGATTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTG-TCGAA
1 TAGTGTCGAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCTCGAA
* * *
382949 ACGGATATTCATAAACATATGATGAATT-CTGTGAATTGCACACT
66 ACTGTTATTCATCAACATATGATGAATTAC-GTGAATTGCACACT
* *
382993 TAGTG-CTGAAATGGTTATTCATCAACATATGATGAATTCCATG-ATCTGCACACTTAGTG-TCG
1 TAGTGTC-GAAACGATTATTCATCAACATATGATGAATTCCATGAAT-TGCACACTTAGTGCTCG
* * * * * *
383055 AAATATGATGAATTCCATGCTGAAACAGTTATTCATCAACATATGATGAATTCCATGATCTGCAC
64 AAA-CTG-T-TATT-CAT-C---AACA--TA-TGATGAA-TTACG-TG-A-------AT-TGCAC
383120 ACT
107 ACT
383123 TAGTGTCGAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGC-CGAA
1 TAGTGTCGAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCTCGAA
* *
383187 A-TGGTTATTCATCAACATATGATGAATTACTTTAATTGCACACT
66 ACT-GTTATTCATCAACATATGATGAATTACGTGAATTGCACACT
* * * * *
383231 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGC
1 TAGTGTCGAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGC
383291 GTAGTTGGTA
Statistics
Matches: 337, Mismatches: 38, Indels: 62
0.77 0.09 0.14
Matches are distributed among these distances:
107 5 0.01
108 212 0.63
109 3 0.01
111 3 0.01
112 3 0.01
116 5 0.01
117 1 0.00
118 4 0.01
119 10 0.03
120 4 0.01
121 2 0.01
122 5 0.01
125 1 0.00
126 3 0.01
127 3 0.01
128 2 0.01
129 3 0.01
130 65 0.19
131 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (109 bp):
TAGTGTCGAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCTCGAA
ACTGTTATTCATCAACATATGATGAATTACGTGAATTGCACACT
Found at i:383058 original size:54 final size:54
Alignment explanation
Indices: 382777--383058 Score: 374
Period size: 54 Copynumber: 5.2 Consensus size: 54
382767 TTTACATACA
* * *
382777 TAGTGCCGAAACGGTTATTCATTAACATATGATGAATTCCGTGAATTGCACACT
1 TAGTGTCGAAATGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACT
* *
382831 TAGTG-CTTAAACT-GTTATTCATCAACATATGATGAATTCCGTGAATTGTACACT
1 TAGTGTC-GAAA-TGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACT
* * * *
382885 TAGTATCGAAATGATTATTCATCAACATATAATGAATTCCATGAATTGCACACT
1 TAGTGTCGAAATGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACT
* * * *
382939 TAGTGTCGAAACGGATATTCATAAACATATGATGAATTCTGTGAATTGCACACT
1 TAGTGTCGAAATGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACT
*
382993 TAGTG-CTGAAATGGTTATTCATCAACATATGATGAATTCCATG-ATCTGCACACT
1 TAGTGTC-GAAATGGTTATTCATCAACATATGATGAATTCCGTGAAT-TGCACACT
383047 TAGTGTCGAAAT
1 TAGTGTCGAAAT
383059 ATGATGAATT
Statistics
Matches: 198, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
53 5 0.03
54 191 0.96
55 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (54 bp):
TAGTGTCGAAATGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACT
Found at i:383070 original size:38 final size:38
Alignment explanation
Indices: 383019--383133 Score: 146
Period size: 38 Copynumber: 3.0 Consensus size: 38
383009 ATTCATCAAC
383019 ATATGATGAATTCCATGATCTGCACACTTAGTGTCGAA
1 ATATGATGAATTCCATGATCTGCACACTTAGTGTCGAA
* * * *
383057 ATATGATGAATTCCATG--CTGAAACAGTTATTCATC-AA
1 ATATGATGAATTCCATGATCTG-CACACTTAGT-GTCGAA
383094 CATATGATGAATTCCATGATCTGCACACTTAGTGTCGAA
1 -ATATGATGAATTCCATGATCTGCACACTTAGTGTCGAA
383133 A
1 A
383134 CGATTATTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
36 3 0.05
37 9 0.14
38 39 0.62
39 9 0.14
40 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (38 bp):
ATATGATGAATTCCATGATCTGCACACTTAGTGTCGAA
Found at i:383142 original size:54 final size:54
Alignment explanation
Indices: 383076--383290 Score: 324
Period size: 54 Copynumber: 4.0 Consensus size: 54
383066 ATTCCATGCT
* *
383076 GAAACAGTTATTCATCAACATATGATGAATTCCATG-ATCTGCACACTTAGTGTC
1 GAAACGGTTATTCATCAACATATGATGAATTCCATGAAT-TGCACACTTAGTGCC
*
383130 GAAACGATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCC
1 GAAACGGTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCC
* * * *
383184 GAAATGGTTATTCATCAACATATGATGAATTACTTTAATTGCACACTTAGTGCC
1 GAAACGGTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCC
* * *
383238 AAAACGGTTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGC
1 GAAACGGTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGC
383291 GTAGTTGGTA
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
54 144 0.99
55 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (54 bp):
GAAACGGTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCC
Found at i:383179 original size:130 final size:130
Alignment explanation
Indices: 382954--383188 Score: 368
Period size: 130 Copynumber: 1.8 Consensus size: 130
382944 TCGAAACGGA
** * *
382954 TATTCATAAACATATGATGAATTCTGTGAATTGCACACTTAGTGCTGAAATGGTTATTCATCAAC
1 TATTCATAAACATATGATGAATTCCATGAATTGCACACTTAGTGCTGAAACGATTATTCATCAAC
*
383019 ATATGATGAATTCCATGATCTGCACACTTAGTGTCGAAATATGATGAATTCCATGCTGAAACAGT
66 ATATGATGAATTCCATGATCTGCACACTTAGTGCCGAAATATGATGAATTCCATGCTGAAACAGT
*
383084 TATTCATCAACATATGATGAATTCCATG-ATCTGCACACTTAGTG-TCGAAACGATTATTCATCA
1 TATTCATAAACATATGATGAATTCCATGAAT-TGCACACTTAGTGCT-GAAACGATTATTCATCA
383147 ACATATGATGAATTCCATGAAT-TGCACACTTAGTGCCGAAAT
64 ACATATGATGAATTCCATG-ATCTGCACACTTAGTGCCGAAAT
383189 GGTTATTCAT
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
129 3 0.03
130 91 0.95
131 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (130 bp):
TATTCATAAACATATGATGAATTCCATGAATTGCACACTTAGTGCTGAAACGATTATTCATCAAC
ATATGATGAATTCCATGATCTGCACACTTAGTGCCGAAATATGATGAATTCCATGCTGAAACAGT
Found at i:383229 original size:184 final size:184
Alignment explanation
Indices: 382899--383235 Score: 554
Period size: 184 Copynumber: 1.8 Consensus size: 184
382889 ATCGAAATGA
382899 TTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGTCGAAACGGATATTCATAAA
1 TTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGTCGAAACGGATATTCATAAA
** *
382964 CATATGATGAATTCTGTGAATTGCACACTTAGTGCTGAAATGGTTATTCATCAACATATGATGAA
66 CATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAA
*
383029 TTCCATGATCTGCACACTTAGTGTCGAAATATGATGAATTCCATGCTGAAACAG
131 TTCCATAATCTGCACACTTAGTGTCGAAATATGATGAATTCCATGCTGAAACAG
* *
383083 TTATTCATCAACATATGATGAATTCCATG-ATCTGCACACTTAGTGTCGAAAC-GATTATTCATC
1 TTATTCATCAACATATAATGAATTCCATGAAT-TGCACACTTAGTGTCGAAACGGA-TATTCATA
383146 AACATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATG
64 AACATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATG
**
383211 AATTACTTTAAT-TGCACACTTAGTG
129 AATT-CCATAATCTGCACACTTAGTG
383236 CCAAAACGGT
Statistics
Matches: 142, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
183 4 0.03
184 134 0.94
185 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (184 bp):
TTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGTCGAAACGGATATTCATAAA
CATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATGAA
TTCCATAATCTGCACACTTAGTGTCGAAATATGATGAATTCCATGCTGAAACAG
Found at i:383262 original size:238 final size:238
Alignment explanation
Indices: 382834--383289 Score: 711
Period size: 238 Copynumber: 1.9 Consensus size: 238
382824 GCACACTTAG
* * * * *
382834 TGCTTAAACTGTTATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTATCGAAATGA
1 TGCTGAAACAGTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTATCGAAACGA
*
382899 TTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGTCGAAACGGATATTCATAAA
66 TTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGCCGAAACGGATATTCATAAA
** *
382964 CATATGATGAATTCTGTGAATTGCACACTTAGTGCTGAAATGGTTATTCATCAACATATGATGAA
131 CATATGATGAATTCTGTGAATTGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAA
383029 TTCCATG-ATCTGCACACTTAGTGTCGAAATATGATGAATTCCA
196 TTCCATGAAT-TGCACACTTAGTGTCGAAATATGATGAATTCCA
*
383072 TGCTGAAACAGTTATTCATCAACATATGATGAATTCCATG-ATCTGCACACTTAGTGTCGAAACG
1 TGCTGAAACAGTTATTCATCAACATATGATGAATTCCATGAAT-TGCACACTTAGTATCGAAACG
* * * *
383136 ATTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATCA
65 ATTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGCCGAAACGGATATTCATAA
*
383201 ACATATGATGAATTACT-TTAATTGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATG
130 ACATATGATGAATT-CTGTGAATTGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATG
* *
383265 AATTCCGTGAATTGTACACTTAGTG
194 AATTCCATGAATTGCACACTTAGTG
383290 CGTAGTTGGT
Statistics
Matches: 198, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
237 2 0.01
238 192 0.97
239 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (238 bp):
TGCTGAAACAGTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTATCGAAACGA
TTATTCATCAACATATAATGAATTCCATGAATTGCACACTTAGTGCCGAAACGGATATTCATAAA
CATATGATGAATTCTGTGAATTGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAA
TTCCATGAATTGCACACTTAGTGTCGAAATATGATGAATTCCA
Done.