Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013775.1 Corchorus capsularis cultivar CVL-1 contig13796, 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: 72318
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:440 original size:31 final size:31
Alignment explanation
Indices: 403--474 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
393 GGTCATGTTT
*
403 AAAGGTTTAGACTCAAATTGAACAAGTTTGA
1 AAAGGTTTAGACTCAAATTGAACAAATTTGA
434 AAAGGTTTAGACTCAAATTGAACAAATTTGA
1 AAAGGTTTAGACTCAAATTGAACAAATTTGA
465 AAAGGTTTAG
1 AAAGGTTTAG
475 CCCCAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.29
Consensus pattern (31 bp):
AAAGGTTTAGACTCAAATTGAACAAATTTGA
Found at i:590 original size:27 final size:29
Alignment explanation
Indices: 528--584 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
518 TATGATTCCA
528 ATAAATTGGTACATTATATAATTTTTAGG
1 ATAAATTGGTACATTATATAATTTTTAGG
557 ATAAATTGGTACATTATATAATTTTTAG
1 ATAAATTGGTACATTATATAATTTTTAG
585 AAAATTACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (29 bp):
ATAAATTGGTACATTATATAATTTTTAGG
Found at i:2600 original size:21 final size:21
Alignment explanation
Indices: 2576--2623 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2566 TTACACTATT
* *
2576 TTTTATGATCCTATTATGAAA
1 TTTTATAATCCTACTATGAAA
* *
2597 TTTTGATAATCTTCCTATGAAA
1 TTTT-ATAATCCTACTATGAAA
2619 TTTTA
1 TTTTA
2624 ATAACGATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (21 bp):
TTTTATAATCCTACTATGAAA
Found at i:2800 original size:22 final size:23
Alignment explanation
Indices: 2746--2806 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
2736 ACTTCCCAAC
*
2746 GAAATTTTGATAACCAACACTAT
1 GAAATATTGATAACCAACACTAT
* **
2769 GAAATGTTGATAACCTCCA-TAT
1 GAAATATTGATAACCAACACTAT
*
2791 GATATATTGATAACCA
1 GAAATATTGATAACCA
2807 CGTTATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (23 bp):
GAAATATTGATAACCAACACTAT
Found at i:2801 original size:45 final size:45
Alignment explanation
Indices: 2721--2806 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
2711 AAGAGCTCAA
* * *
2721 TATGAAATTTTGATAACTTCCCAACGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCTCCCAACGAAATATTGATAACCAACAC
* *
2766 TATGAAATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ACGAAATATTGATAACCA
2807 CGTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAACGAAATATTGATAACCAACAC
Found at i:2866 original size:22 final size:22
Alignment explanation
Indices: 2841--2909 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
2831 GAATTGTTAG
*
2841 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
2863 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
2885 TAATCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
2907 TAA
1 TAA
2910 ATATTCCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:2941 original size:23 final size:22
Alignment explanation
Indices: 2854--2944 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 22
2844 TCACACTCTG
* * *
2854 AAATTTTGATAATCACACTATG
1 AAATTTTGATAATCTCCCTATA
* * *
2876 AAATTGTGATAATCTCGCTATG
1 AAATTTTGATAATCTCCCTATA
* *
2898 AAATTTTGATAAATATTCCTATA
1 AAATTTTGAT-AATCTCCCTATA
*
2921 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AATCTCCCTATA
2944 A
1 A
2945 CTTTCTTACG
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
22 28 0.49
23 29 0.51
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAATCTCCCTATA
Found at i:3021 original size:22 final size:22
Alignment explanation
Indices: 2971--3132 Score: 118
Period size: 22 Copynumber: 7.5 Consensus size: 22
2961 TGATAACTGC
*
2971 AAATTTTGATAACCTCTCTATG
1 AAATTTTGATAACCTCACTATG
** *
2993 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCACTATG
* ** * *
3015 AAATTTTGTTAATATCCCTATA
1 AAATTTTGATAACCTCACTATG
* *
3037 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCACTATG
*
3059 AAATTTTGATAACCCTC-TTATG
1 AAATTTTGATAA-CCTCACTATG
* *
3081 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CACTATG
* *
3103 AAATTTTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCACTATG
3123 AAATTTTGAT
1 AAATTTTGAT
3133 TACTCCATAA
Statistics
Matches: 107, Mismatches: 27, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
20 14 0.13
21 4 0.04
22 83 0.78
23 6 0.06
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:3439 original size:22 final size:22
Alignment explanation
Indices: 3213--3467 Score: 123
Period size: 22 Copynumber: 11.6 Consensus size: 22
3203 AGAAATACTA
3213 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
3236 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
3257 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
3279 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
* *
3301 CTATGAAATTCTCATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
**
3324 -TATCTAATTTTGATAA-C-CT
1 CTATGAAATTTTGATAATCACT
* * *
3343 CGTTTTGAAATTTTGATAATAACA
1 C--TATGAAATTTTGATAATCACT
***
3367 CTATGAAATTTTGATAATGTTT
1 CTATGAAATTTTGATAATCACT
*
3389 CTA-AAAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATC--A-CT
*
3413 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
3435 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
*
3455 CTATCAAATTTTG
1 CTATGAAATTTTG
3468 GTACACCTTA
Statistics
Matches: 176, Mismatches: 42, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
19 2 0.01
20 9 0.05
21 30 0.17
22 114 0.65
23 2 0.01
24 6 0.03
25 13 0.07
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:3520 original size:22 final size:21
Alignment explanation
Indices: 3490--3628 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
3480 AAATTGAGAC
3490 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
3511 TTTTGATAACCACAGTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
3533 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
3555 TATT-AGTAA-CTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* *
3576 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
3598 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
3620 TTTTGATAA
1 TTTTGATAA
3629 TCTCTTTGAT
Statistics
Matches: 91, Mismatches: 16, Indels: 21
0.71 0.12 0.16
Matches are distributed among these distances:
20 2 0.02
21 23 0.25
22 62 0.68
23 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:3585 original size:21 final size:20
Alignment explanation
Indices: 3530--3581 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
3520 CCACAGTATA
*
3530 AAATTTTGATAACCTCCCCATG
1 AAATTTTG-TAA-CTCCCAATG
* *
3552 AAATATTAGTAACTCCTAATG
1 AAAT-TTTGTAACTCCCAATG
3573 AAATTTTGT
1 AAATTTTGT
3582 TAACCACACT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 7 0.28
23 3 0.12
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (20 bp):
AAATTTTGTAACTCCCAATG
Found at i:3744 original size:22 final size:22
Alignment explanation
Indices: 3718--3774 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
3708 TAATTTGATC
3718 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
3740 CTATGAAATTTTGGTAATCACA
1 CTATGAAATTTTGGTAACCACA
*
3762 CTATGGAATTTTG
1 CTATGAAATTTTG
3775 ATAAACTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:3793 original size:22 final size:22
Alignment explanation
Indices: 3718--3793 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
3708 TAATTTGATC
*
3718 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAAACACA
*
3740 CTATGAAATTTTGGTAATCACA
1 CTATGAAATTTTGGTAAACACA
* * *
3762 CTATGGAATTTTGATAAACTC-
1 CTATGAAATTTTGGTAAACACA
3783 CTCATGAAATT
1 CT-ATGAAATT
3794 ATAATAACCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 2 0.04
22 45 0.96
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGGTAAACACA
Found at i:4047 original size:19 final size:20
Alignment explanation
Indices: 4016--4053 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4006 TATTGACATT
4016 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
4035 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
4054 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:5922 original size:40 final size:40
Alignment explanation
Indices: 5862--5941 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
5852 AACTAATGAC
* * *
5862 TTTCGTTTCTTAACTAAATTTTCTTAAAAGCACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTCATAAA
*
5902 TTTCATTTCTTAACTGAATTTTCTTAAAAGAACTCATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTCATAAA
5942 ATAAAACAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (40 bp):
TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTCATAAA
Found at i:28935 original size:130 final size:133
Alignment explanation
Indices: 28794--29039 Score: 408
Period size: 130 Copynumber: 1.9 Consensus size: 133
28784 GCAGGAATCG
* *
28794 AAACCAATACAATAATTGCTTGTGTTAATTCAATAGAGGTCATTTAGAAATTTCAACTCTAATTC
1 AAACCAATACAATAATTGCTTGTGTTAATTCAATAGAGGTCATTTAAAAATTTCAACTCTAAGTC
**
28859 AGAACAAACTGTCAAAAG-AAAAAA-AAGCAGAGAA-AATAAATTAAGAACTCAAATTGTAGGAA
66 AGAACAAACTGTCAAAAGAAAAAAACAAAAAGAGAATAATAAATTAAGAACTCAAATTGTAGGAA
28921 CCA
131 CCA
*
28924 AAACCAATACAATAGTTGCTTGTGTTAATTCAATAGAGGTCATTTAAAAATTTCAACTCTAAGTC
1 AAACCAATACAATAATTGCTTGTGTTAATTCAATAGAGGTCATTTAAAAATTTCAACTCTAAGTC
* *
28989 ATAACAAACTGTTAAAAGAAAAAAACAAAAAGAGAATAATAAATTAAGAAC
66 AGAACAAACTGTCAAAAGAAAAAAACAAAAAGAGAATAATAAATTAAGAAC
29040 GAAAAGCTCA
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
130 78 0.74
131 6 0.06
132 8 0.08
133 14 0.13
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (133 bp):
AAACCAATACAATAATTGCTTGTGTTAATTCAATAGAGGTCATTTAAAAATTTCAACTCTAAGTC
AGAACAAACTGTCAAAAGAAAAAAACAAAAAGAGAATAATAAATTAAGAACTCAAATTGTAGGAA
CCA
Found at i:29302 original size:2 final size:2
Alignment explanation
Indices: 29295--29322 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29285 AAAGATAAAG
29295 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
29323 TCATTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30147 original size:59 final size:57
Alignment explanation
Indices: 30055--30185 Score: 192
Period size: 59 Copynumber: 2.3 Consensus size: 57
30045 TTATCCCATT
* * *
30055 CTTCATATTTTCTTCTTCTCCATATTTTATTGTCTCTCTATTCTCTTGTCTTTTACATA
1 CTTCATATTTTCTTCTTCTACATATTCTATTGTCTCTCTATTCTC--GTCTTTAACATA
*
30114 CTTCATATTTTCTTCTTCTACATATTCTATTGTCTCTCTATTCTCGTCTTTAATATA
1 CTTCATATTTTCTTCTTCTACATATTCTATTGTCTCTCTATTCTCGTCTTTAACATA
30171 CTTCA-ATTTTACTTC
1 CTTCATATTTT-CTTC
30186 ATTGCTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
56 5 0.07
57 19 0.28
59 43 0.64
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.56
Consensus pattern (57 bp):
CTTCATATTTTCTTCTTCTACATATTCTATTGTCTCTCTATTCTCGTCTTTAACATA
Found at i:30282 original size:46 final size:46
Alignment explanation
Indices: 30215--30310 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
30205 ATTTCACAAC
30215 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
1 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
30261 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
1 AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
30307 AAAA
1 AAAA
30311 CAGCGGCCGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (46 bp):
AAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
Found at i:31182 original size:33 final size:33
Alignment explanation
Indices: 31140--31207 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
31130 GTGTTGTAAC
*
31140 TTCGGATATCCCAGGAATTAATTAAACAAATAA
1 TTCGGATATCCCAGGAATTAATCAAACAAATAA
31173 TTCGGATATCCCAGGAATTAATCAAACAAATAA
1 TTCGGATATCCCAGGAATTAATCAAACAAATAA
31206 TT
1 TT
31208 AAAGCAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TTCGGATATCCCAGGAATTAATCAAACAAATAA
Found at i:32999 original size:31 final size:31
Alignment explanation
Indices: 32954--33070 Score: 164
Period size: 31 Copynumber: 3.8 Consensus size: 31
32944 CCATGAGTAA
*
32954 CCACCAAAGGTATACCGTAAACACCTAATAC
1 CCACCAAAGGTATACCGTAAACACCTACTAC
* * * *
32985 CCACCGAAGATATACCCTAAACACCCACTAC
1 CCACCAAAGGTATACCGTAAACACCTACTAC
*
33016 CCACCAAAGGTATATCGTAAACACCTACTAC
1 CCACCAAAGGTATACCGTAAACACCTACTAC
*
33047 CCA-CGAAGGTATACCGTAAACACC
1 CCACCAAAGGTATACCGTAAACACC
33071 CACCAAATAT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 19 0.26
31 55 0.74
ACGTcount: A:0.39, C:0.35, G:0.10, T:0.15
Consensus pattern (31 bp):
CCACCAAAGGTATACCGTAAACACCTACTAC
Found at i:33027 original size:62 final size:61
Alignment explanation
Indices: 32954--33073 Score: 195
Period size: 62 Copynumber: 2.0 Consensus size: 61
32944 CCATGAGTAA
32954 CCACCAAAGGTATACCGTAAACACCTAATACCCACCGAAGATATACCCTAAACACCCACTAC
1 CCACCAAAGGTATACCGTAAACACCTAATACCCA-CGAAGATATACCCTAAACACCCACTAC
* * * *
33016 CCACCAAAGGTATATCGTAAACACCTACTACCCACGAAGGTATACCGTAAACACCCAC
1 CCACCAAAGGTATACCGTAAACACCTAATACCCACGAAGATATACCCTAAACACCCAC
33074 CAAATATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
61 22 0.41
62 32 0.59
ACGTcount: A:0.39, C:0.36, G:0.10, T:0.15
Consensus pattern (61 bp):
CCACCAAAGGTATACCGTAAACACCTAATACCCACGAAGATATACCCTAAACACCCACTAC
Found at i:33587 original size:36 final size:34
Alignment explanation
Indices: 33540--33655 Score: 135
Period size: 36 Copynumber: 3.3 Consensus size: 34
33530 ACAAGGGGGC
*
33540 ACGCCCCCCTTCCAATCTAATATGGGGAGAGGCGTT
1 ACGCCCCCCTTCCAATCT-ATATGGGG-GAGGCATT
* *
33576 ACGCCCCCCTTCCAATTTTTAATGGGGGTAGGCATT
1 ACGCCCCCCTTCCAATCTAT-ATGGGGG-AGGCATT
*
33612 ACGCCCCCCTTAACAATCTA-ATGGGGGAGGCATT
1 ACGCCCCCCTT-CCAATCTATATGGGGGAGGCATT
33646 ACGCCACCCC
1 ACGCC-CCCC
33656 CCTGCAATCC
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
34 12 0.17
35 13 0.19
36 40 0.57
37 5 0.07
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (34 bp):
ACGCCCCCCTTCCAATCTATATGGGGGAGGCATT
Found at i:34251 original size:31 final size:31
Alignment explanation
Indices: 34207--34294 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
34197 CCATGAGTAA
*
34207 CCACCAAAGGTATACCGTAAACACCTACTAC
1 CCACCAAAGGTATACCGTAAACACCCACTAC
* *
34238 CCGCCGAAGGTATACCGTAAACACCCACTAC
1 CCACCAAAGGTATACCGTAAACACCCACTAC
34269 CCACCAAAGGTATACCGTAAACACCC
1 CCACCAAAGGTATACCGTAAACACCC
34295 GCCAAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.36, C:0.38, G:0.12, T:0.14
Consensus pattern (31 bp):
CCACCAAAGGTATACCGTAAACACCCACTAC
Found at i:37068 original size:45 final size:44
Alignment explanation
Indices: 36993--37093 Score: 139
Period size: 45 Copynumber: 2.3 Consensus size: 44
36983 CAATCTTCCC
* *
36993 ATGAAATTTTGTCAACCTTCCTATAGAATTTTGAAAACCTCACT
1 ATGAAATTTTGTAAACCTTCCTATAAAATTTTGAAAACCTCACT
* **
37037 ATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAACCTCTTT
1 ATGAAATTTTG-TAAACCTTCCTATAAAATTTTGAAAACCTCACT
*
37082 GTGAAATTTTGT
1 ATGAAATTTTGT
37094 TTACCTCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
44 12 0.24
45 38 0.76
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (44 bp):
ATGAAATTTTGTAAACCTTCCTATAAAATTTTGAAAACCTCACT
Found at i:37088 original size:22 final size:22
Alignment explanation
Indices: 36859--37244 Score: 101
Period size: 22 Copynumber: 17.8 Consensus size: 22
36849 ATAATTACAT
* *
36859 TATGAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCTCTC
* * *
36881 TCTGAAAATTTTGATAGCAT-TC
1 TATG-AAATTTTGATAACCTCTC
* * *
36903 TTATTAAATTTTGATAACGAT-AC
1 -TATGAAATTTTGATAAC-CTCTC
* * * * *
36926 TATGCAATTTCGAGAACTTCCC
1 TATGAAATTTTGATAACCTCTC
* * * *
36948 TATGAAATGTCGAGAACCTTTC
1 TATGAAATTTTGATAACCTCTC
* *
36970 TATGAAATTTT-TTCAATCT-TCC
1 TATGAAATTTTGAT-AACCTCT-C
*
36992 CATGAAATTTTG-TCAACCT-TCC
1 TATGAAATTTTGAT-AACCTCT-C
* *
37014 TAT-AGAATTTTGAAAACCTCAC
1 TATGA-AATTTTGATAACCTCTC
37036 TATGAAATTTTGATAAACCT-TCC
1 TATGAAATTTTGAT-AACCTCT-C
* *
37059 TATAAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTC
* * * *
37081 TGTGAAATTTTGTTTACCTCTAA
1 TATGAAATTTTGATAACCTCT-C
*
37104 TCTG---TTTTGAT-A-C-C-C
1 TATGAAATTTTGATAACCTCTC
* * *
37119 TATGAAATTTTGATCTA-CACAC
1 TATGAAATTTTGAT-AACCTCTC
* * *
37141 TATCAAATTTT-A-AACCACAC
1 TATGAAATTTTGATAACCTCTC
* *
37161 TATAAAATTTTGATAATCTCTC
1 TATGAAATTTTGATAACCTCTC
* **
37183 TAT-AGAATTTTGA-AAACTAAAC
1 TATGA-AATTTTGATAACCT-CTC
** *
37205 TATGAAATTTCAATAACCTCCC
1 TATGAAATTTTGATAACCTCTC
* *
37227 GATAAAATTTTGATAACC
1 TATGAAATTTTGATAACC
37245 AAAAGCCTTT
Statistics
Matches: 274, Mismatches: 61, Indels: 58
0.70 0.16 0.15
Matches are distributed among these distances:
15 3 0.01
17 1 0.00
18 8 0.03
19 2 0.01
20 23 0.08
21 11 0.04
22 180 0.66
23 46 0.17
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTC
Found at i:37558 original size:26 final size:26
Alignment explanation
Indices: 37529--37579 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
37519 ATGGTAAGGT
* *
37529 AGAAATTGAACATTTCTAAGTAAAAC
1 AGAAATTGAAAATTTCTAAATAAAAC
37555 AGAAATTGAAAATTTCTAAATAAAA
1 AGAAATTGAAAATTTCTAAATAAAA
37580 TATTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (26 bp):
AGAAATTGAAAATTTCTAAATAAAAC
Found at i:37743 original size:27 final size:27
Alignment explanation
Indices: 37708--37816 Score: 92
Period size: 27 Copynumber: 4.3 Consensus size: 27
37698 ACACAAAATC
37708 ATATATTTTAATAATGGCATAA-TTA-AA
1 ATATATTTTAATAATGG--TAATTTAGAA
*
37735 ATATATTTTGATAATGGTAATTTAGAA
1 ATATATTTTAATAATGGTAATTTAGAA
* *
37762 ATATA-TTT-AT-TTTGTAA---A-AA
1 ATATATTTTAATAATGGTAATTTAGAA
**
37782 ATATATTTTAATAATGACAATTTAGAA
1 ATATATTTTAATAATGGTAATTTAGAA
37809 ATATATTT
1 ATATATTT
37817 GAAAGAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
20 7 0.11
21 4 0.06
22 2 0.03
23 3 0.05
24 5 0.08
25 5 0.08
26 7 0.11
27 33 0.50
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (27 bp):
ATATATTTTAATAATGGTAATTTAGAA
Found at i:37875 original size:2 final size:2
Alignment explanation
Indices: 37868--37902 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
37858 ATTTGTTACT
*
37868 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37903 TTGCACTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42442 original size:19 final size:19
Alignment explanation
Indices: 42418--42456 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42408 TCGAGCTAGG
42418 AGTCGTGCGTTTGGTTACT
1 AGTCGTGCGTTTGGTTACT
42437 AGTCGTGCGTTTGGTTACT
1 AGTCGTGCGTTTGGTTACT
42456 A
1 A
42457 TAGACACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.13, C:0.15, G:0.31, T:0.41
Consensus pattern (19 bp):
AGTCGTGCGTTTGGTTACT
Found at i:44044 original size:347 final size:349
Alignment explanation
Indices: 43182--44226 Score: 1375
Period size: 347 Copynumber: 3.0 Consensus size: 349
43172 TCCAAAACAT
* * * *
43182 TCTCCAAGTCGGTTTAGGAAAAGATTAATTATATCCAGAAATTTCAAGGGCAAAATCGTCCACCA
1 TCTCCAAGTCGGTTTAGGAGAAGATCAATTATGTCCAGAAATTTCAAGGGCAAAATCATCCACCA
* * *
43247 AAAATGCAGAATTAGGTCTCGAGGTAACATAAAAGTTCTAGATATTGGAAACCTCTTTTCAACAG
66 GAAATGCAGAATTAGGTCTCGAGGTAACATAAAAGTTCTAGATATTGGAATCCTCTTTCCAACAG
* *
43312 TACCTCATTTGCATTTTTCTGAGTTTTGGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTT
131 TACCTCATTTGCATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTT
* ** * * * *
43377 GTGAAGTCCTATTTTGAATTTGATTTAACAATGCCGCATTAGGACTGAATCATTACTGCTTCATA
196 GTGAAGTCCTCTTTTGAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTGCATCATA
**
43442 ATTAC-AGATTGGACTTGAACTCCTTCTTTGACCTTCCATATTAACGAATTGGGTCTAAGAATAT
261 ATTACTA-ATTGGACTTGAACTCC-TCTTTGGGCTTCCATATTAACGAATTGGGTCTAAGAATAT
*
43506 CAAATTTAGCCTTCAAGACATCTGGC
324 CAAATTTAGACTTCAAGACATCTGGC
** *
43532 TCTCCAAGTCCATTTAGGAGAAGATCAATTATATGTCGAGAAATTTCAAGGGCAAAATCATCCAC
1 TCTCCAAGTCGGTTTAGGAGAAGATCAA-T-TATGTCCAGAAATTTCAAGGGCAAAATCATCCAC
* * * * * *
43597 CGGAACTGCAGAATCAGGTCTCGAGG--ACATAAAAGTTGTAGATATTGGAATCCTCATTCCAAA
64 CAGAAATGCAGAATTAGGTCTCGAGGTAACATAAAAGTTCTAGATATTGGAATCCTCTTTCCAAC
* ** *
43660 AGTACCTCATTTGCATTTTTCTAAGCTCTAAATCAAAAGTTATGAATTTTCTTCCAAAACCGCTC
129 AGTACCTCATTTGCATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTC
* * * *
43725 TTGTGAAGTCCTCTTTTCAATAGGATTTAACAATGTTGCATCAGGGCTGAATCATTATTACATCA
194 TTGTGAAGTCCTCTTTTGAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTGCATCA
* *
43790 TAATTACTAATTGGACTTGGACT-C-CTTTGGGCTTCCATATTAACGAATTGGGCCTAAGAATAT
259 TAATTACTAATTGGACTTGAACTCCTCTTTGGGCTTCCATATTAACGAATTGGGTCTAAGAATAT
*
43853 CATATTTAGACTTCAAGACATCTGGC
324 CAAATTTAGACTTCAAGACATCTGGC
* * * *
43879 TCTCCAAGTTGGTTTAGGAGAAGATCAATTCTGTCTAGAAATGTCAAGGGCAAAATCATCCACCA
1 TCTCCAAGTCGGTTTAGGAGAAGATCAATTATGTCCAGAAATTTCAAGGGCAAAATCATCCACCA
** * * * * * **
43944 GAAATATAGAATTAGGTCTTG-GGATAACATAAAATTTTTAGATGTTGGAGTTTTCTTTCCAAC-
66 GAAATGCAGAATTAGGTCTCGAGG-TAACATAAAAGTTCTAGATATTGGAATCCTCTTTCCAACA
* * *
44007 GATACCTCATTTGAATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTTCTTACAAAAATGCTC
130 G-TACCTCATTTGCATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTC
* * * *
44072 TTGTGAAGTCTTCCTTTGAATAGGATTTAACAATGCTGCATCACGGCTAAATCATTACTGCATCA
194 TTGTGAAGTCCTCTTTTGAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTGCATCA
* * * * *
44137 TAATTACTGATTGGACTTGCACTCCTTCTTTGGGCTTCCATATTAAGGAATTGGATCTAAAAATA
259 TAATTACTAATTGGACTTGAACTCC-TCTTTGGGCTTCCATATTAACGAATTGGGTCTAAGAATA
** *
44202 TCGGATTTAGACTTCAAGATATCTG
323 TCAAATTTAGACTTCAAGACATCTG
44227 ACTTAACAAT
Statistics
Matches: 602, Mismatches: 83, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
344 2 0.00
345 48 0.08
346 2 0.00
347 248 0.41
348 1 0.00
349 1 0.00
350 245 0.41
351 2 0.00
352 53 0.09
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (349 bp):
TCTCCAAGTCGGTTTAGGAGAAGATCAATTATGTCCAGAAATTTCAAGGGCAAAATCATCCACCA
GAAATGCAGAATTAGGTCTCGAGGTAACATAAAAGTTCTAGATATTGGAATCCTCTTTCCAACAG
TACCTCATTTGCATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTT
GTGAAGTCCTCTTTTGAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTGCATCATA
ATTACTAATTGGACTTGAACTCCTCTTTGGGCTTCCATATTAACGAATTGGGTCTAAGAATATCA
AATTTAGACTTCAAGACATCTGGC
Found at i:49293 original size:6 final size:6
Alignment explanation
Indices: 49284--49345 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
49274 TTTCTATTTC
* *
49284 CCTTTT CCTTTT CC-TTT --TTTT CTTTTT CCTTTT CCTTTT -GTTTT
1 CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT
*
49328 -CTTTT TCTTTT CCCTTTT
1 CCTTTT CCTTTT -CCTTTT
49346 TTTTTTCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 3 0.06
5 11 0.23
6 28 0.60
7 5 0.11
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.73
Consensus pattern (6 bp):
CCTTTT
Found at i:49310 original size:15 final size:15
Alignment explanation
Indices: 49286--49316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49276 TCTATTTCCC
49286 TTTTCCTTTTCCTTT
1 TTTTCCTTTTCCTTT
*
49301 TTTTCTTTTTCCTTT
1 TTTTCCTTTTCCTTT
49316 T
1 T
49317 CCTTTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCCTTTTCCTTT
Found at i:49311 original size:21 final size:21
Alignment explanation
Indices: 49286--49348 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 21
49276 TCTATTTCCC
49286 TTTTCCTTTTCCTTTTTTTCT
1 TTTTCCTTTTCCTTTTTTTCT
49307 TTTTCCTTTTCCTTTTGTTTTCT
1 TTTTCCTTTTCC-TTT-TTTTCT
49330 TTTT-CTTTTCCCTTTTTTT
1 TTTTCCTTTT-CCTTTTTTT
49349 TTTCTTCTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
21 16 0.41
22 11 0.28
23 12 0.31
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCCTTTTCCTTTTTTTCT
Found at i:49311 original size:28 final size:27
Alignment explanation
Indices: 49273--49354 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
49263 TTTATTATTA
*
49273 TTTTCTATTTCCCTTTTCCTTTTCCTTT
1 TTTTCTTTTTCCCTTTTCCTTTT-CTTT
*
49301 TTTTCTTTTT-CCTTTTCCTTTTGTTT
1 TTTTCTTTTTCCCTTTTCCTTTTCTTT
* **
49327 TCTTTTTCTTTTCCCTTTTTTTTTTCTT
1 T-TTTCT-TTTTCCCTTTTCCTTTTCTT
49355 CTGTTGGGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 16 0.36
28 13 0.29
29 12 0.27
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (27 bp):
TTTTCTTTTTCCCTTTTCCTTTTCTTT
Found at i:49331 original size:23 final size:22
Alignment explanation
Indices: 49286--49349 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 22
49276 TCTATTTCCC
49286 TTTTCCTTTTCC-TTTTTTTCT
1 TTTTCCTTTTCCTTTTTTTTCT
49307 TTTTCCTTTTCCTTTTGTTTTCT
1 TTTTCCTTTTCCTTTT-TTTTCT
49330 TTTT-CTTTTCCCTTTTTTTT
1 TTTTCCTTTT-CCTTTTTTTT
49350 TTCTTCTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 12 0.30
22 12 0.30
23 16 0.40
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTCCTTTTCCTTTTTTTTCT
Found at i:49333 original size:17 final size:16
Alignment explanation
Indices: 49292--49338 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
49282 TCCCTTTTCC
49292 TTTTCCTTTT-TTTCT-
1 TTTTCCTTTTCTTT-TG
49307 TTTTCCTTTTCCTTTTG
1 TTTTCCTTTT-CTTTTG
*
49324 TTTTCTTTTTCTTTT
1 TTTTCCTTTTCTTTT
49339 CCCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.36
16 6 0.21
17 12 0.43
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTCCTTTTCTTTTG
Found at i:49346 original size:13 final size:13
Alignment explanation
Indices: 49273--49352 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
49263 TTTATTATTA
49273 TTTTCTATTTCCCT
1 TTTTCT-TTTCCCT
* *
49287 TTTCCTTTTCCTTT
1 TTTTCTTTTCC-CT
*
49301 TTTTCTTTTTCCT
1 TTTTCTTTTCCCT
* **
49314 TTTCCTTTTGTTTTCT
1 TTT--TCTT-TTCCCT
49330 TTTTCTTTTCCCT
1 TTTTCTTTTCCCT
*
49343 TTTTTTTTTC
1 TTTTCTTTTC
49353 TTCTGTTGGG
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
13 22 0.43
14 18 0.35
15 3 0.06
16 8 0.16
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.74
Consensus pattern (13 bp):
TTTTCTTTTCCCT
Found at i:49356 original size:21 final size:19
Alignment explanation
Indices: 49286--49356 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 19
49276 TCTATTTCCC
*
49286 TTTTCCTTTTCCTTTTTTT
1 TTTTTCTTTTCCTTTTTTT
49305 CTTTTTCCTTTTCCTTTTGTTTT
1 -TTTTT-CTTTTCC-TTT-TTTT
49328 CTTTTTCTTTTCCCTTTTTTT
1 -TTTTTCTTTT-CCTTTTTTT
49349 TTTCTTCT
1 TTT-TTCT
49357 GTTGGGCCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
20 7 0.16
21 15 0.33
22 11 0.24
23 12 0.27
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTTCTTTTCCTTTTTTT
Found at i:51761 original size:179 final size:178
Alignment explanation
Indices: 51323--51982 Score: 471
Period size: 180 Copynumber: 3.7 Consensus size: 178
51313 AAAAGAAAAA
** * * * * * *
51323 GAAACATCAAATTTAGAATTCAAATTCTTC-ATGAAAGTTGTAGATCATGAAACAACCTTTAAAC
1 GAAACATCAAATTTAGCTTTCAAA-TCCTCAATAAAAGTTGTAGATAATGGAACAACCTTTTAAT
* * * * * * ** * * *
51387 AAATACTTAAACCACCTTAATAAGAAATCTAGAG-AAAAAAT-TTTGTAATATAAAGTAGACCAT
65 AGACACTTGAATCATCTCAATCGGACATCTAGAGAAAAAAATATATGTAATATTAAGTAG-CCAT
* * * ** * *
51450 CCATT-ATCGCTAACCGAAACAACTAATTTTTCGAAAGCATTATTTAGGATACTT
129 TCATTCAT-ACTAACCGAAA-AACAAAGGTTTCAAAAGCA-T-TTT-CGATACTT
* * ** * * * * ** * * *
51504 GTAACATCAAATTCAATTTTCCAGTCCT-GATAAAAATTCCAGATCATAGAACAACCTTTTGATA
1 GAAACATCAAATTTAGCTTTCAAATCCTCAATAAAAGTTGTAGATAATGGAACAACCTTTTAATA
* * * *
51568 GACACTTAAATCATCTCAATCGGATATCTAGAGAAAAAAATATATGTAATATTTAGTAGGC-TGT
66 GACACTTGAATCATCTCAATCGGACATCTAGAGAAAAAAATATATGTAATATTAAGTAGCCAT-T
* *
51632 CAATTCCA-ACTAACGGAAAAACTAAGGTTTCAAAAGCATTTT-GAATACTT
130 C-ATT-CATACTAACCGAAAAACAAAGGTTTCAAAAGCATTTTCG-ATACTT
** * * *
51682 GAAACATCAAATTTAGCTTTTGAGTCC-CACATAAAAGTTTTAGATAATGGAACAACCATTTAAT
1 GAAACATCAAATTTAGCTTTCAAATCCTCA-ATAAAAGTTGTAGATAATGGAACAACCTTTTAAT
* * * *
51746 AGACACTTGAATCATCTCAATTGGACATCTACAGAAAAAAAAATTATGTAATATTAAGTAAACCA
65 AGACACTTGAATCATCTCAATCGGACATCTAGAGAAAAAAATA-TATGTAATATTAAGT-AGCCA
* * * ***
51811 TTCATTTATGCTAACCGAAAAACAAAGTTTTGGGAAGCATTTTCGATACTT
128 TTCATTCATACTAACCGAAAAACAAAGGTTTCAAAAGCATTTTCGATACTT
* * * * *
51862 GAAACATCATATTTAGCTTTCAAATCCTTAATGAAAGTTGTAGATCATGGAACAAACTTTTAATA
1 GAAACATCAAATTTAGCTTTCAAATCCTCAATAAAAGTTGTAGATAATGGAACAACCTTTTAATA
* * * * * *
51927 AAAACTTGAATCACCCCAATCGGACATGTAGAG--CAAAAT-TATGTAATATTAAGTAG
66 GACACTTGAATCATCTCAATCGGACATCTAGAGAAAAAAATATATGTAATATTAAGTAG
51983 ATTGTCCATA
Statistics
Matches: 378, Mismatches: 85, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
175 1 0.00
176 15 0.04
177 1 0.00
178 31 0.08
179 69 0.18
180 185 0.49
181 48 0.13
182 27 0.07
184 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (178 bp):
GAAACATCAAATTTAGCTTTCAAATCCTCAATAAAAGTTGTAGATAATGGAACAACCTTTTAATA
GACACTTGAATCATCTCAATCGGACATCTAGAGAAAAAAATATATGTAATATTAAGTAGCCATTC
ATTCATACTAACCGAAAAACAAAGGTTTCAAAAGCATTTTCGATACTT
Found at i:51862 original size:180 final size:177
Alignment explanation
Indices: 51421--51981 Score: 483
Period size: 180 Copynumber: 3.1 Consensus size: 177
51411 AAATCTAGAG
* * * * *
51421 AAAAAATTTTGTAATATAAAGTAGACCATCCA-TTATCGCTAACCGAAACAACTAATTTTTCGAA
1 AAAAAATTATGTAATATTAAGTAAACCATTCATTTAT-GCTAACCGAAA-AACTAAGTTTTCGAA
* * * * ** * *
51485 AGCATTATTTAGGATACTTGTAACATCAAATTCA-ATTTTCCAGTCCTGATAAAAATTCCAGATC
64 AGCA-T-TTT--GATACTTGAAACATCAAATTTAGCTTTT-AAGTCCCAATAAAAGTTCTAGATC
* * * * *
51549 ATAGAACAACCTTTTGATAGACACTTAAATCATCTCAATCGGATATCT-AGAGA
124 ATGGAACAACCTTTTAATAGACACTTGAATCATCTCAATCGGACATCTAAGAAA
* ** * * * * *
51602 AAAAAATATATGTAATATTTAGT-AGGC-TGTCAATTCCA-ACTAACGGAAAAACTAAGGTTTCA
1 AAAAAAT-TATGTAATATTAAGTAAACCAT-TC-ATT-TATGCTAACCGAAAAACTAAGTTTTCG
* * *
51664 AAAGCATTTTGAATACTTGAAACATCAAATTTAGCTTTTGAGTCCCACATAAAAGTTTTAGATAA
62 AAAGCATTTTG-ATACTTGAAACATCAAATTTAGCTTTTAAGTCCCA-ATAAAAGTTCTAGATCA
* *
51729 TGGAACAACCATTTAATAGACACTTGAATCATCTCAATTGGACATCTACAGAAA
125 TGGAACAACCTTTTAATAGACACTTGAATCATCTCAATCGGACATCTA-AGAAA
* * *
51783 AAAAAATTATGTAATATTAAGTAAACCATTCATTTATGCTAACCGAAAAACAAAGTTTTGGGAAG
1 AAAAAATTATGTAATATTAAGTAAACCATTCATTTATGCTAACCGAAAAACTAAGTTTTCGAAAG
* * * * * *
51848 CATTTTCGATACTTGAAACATCATATTTAGCTTTCAAATCCTTAATGAAAGTTGTAGATCATGGA
66 CATTTT-GATACTTGAAACATCAAATTTAGCTTTTAAGTCC-CAATAAAAGTTCTAGATCATGGA
* * * * * *
51913 ACAAACTTTTAATAAAAACTTGAATCACCCCAATCGGACATGT-AG--A
129 ACAACCTTTTAATAGACACTTGAATCATCTCAATCGGACATCTAAGAAA
**
51959 GCAAAATTATGTAATATTAAGTA
1 AAAAAATTATGTAATATTAAGTA
51982 GATTGTCCAT
Statistics
Matches: 306, Mismatches: 59, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
176 22 0.07
177 1 0.00
178 26 0.08
179 62 0.20
180 128 0.42
181 42 0.14
182 23 0.08
183 1 0.00
184 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (177 bp):
AAAAAATTATGTAATATTAAGTAAACCATTCATTTATGCTAACCGAAAAACTAAGTTTTCGAAAG
CATTTTGATACTTGAAACATCAAATTTAGCTTTTAAGTCCCAATAAAAGTTCTAGATCATGGAAC
AACCTTTTAATAGACACTTGAATCATCTCAATCGGACATCTAAGAAA
Found at i:59397 original size:19 final size:19
Alignment explanation
Indices: 59373--59409 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
59363 AATGCTTTAG
59373 ATTAATGCATGCCAAATTA
1 ATTAATGCATGCCAAATTA
*
59392 ATTAATGCATGCTAAATT
1 ATTAATGCATGCCAAATT
59410 GAGAGCCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (19 bp):
ATTAATGCATGCCAAATTA
Found at i:59624 original size:2 final size:2
Alignment explanation
Indices: 59608--59653 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
59598 TTCTTATTAT
*
59608 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA CTA TA -A TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
59648 TA TA TA
1 TA TA TA
59654 ATCTATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:59634 original size:22 final size:23
Alignment explanation
Indices: 59608--59661 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
59598 TTCTTATTAT
*
59608 TATATTATAATATATATATATATA
1 TATA-TATAATATAAATATATATA
59632 TATACTATAATATAAATATATA-A
1 TATA-TATAATATAAATATATATA
*
59655 TCTATAT
1 TATATAT
59662 TATTGTATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 4 0.15
24 20 0.74
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TATATATAATATAAATATATATA
Found at i:59640 original size:24 final size:24
Alignment explanation
Indices: 59608--59653 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
59598 TTCTTATTAT
* *
59608 TATATTATAATATATATATATATA
1 TATACTATAATATAAATATATATA
59632 TATACTATAATATAAATATATA
1 TATACTATAATATAAATATATA
59654 ATCTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATACTATAATATAAATATATATA
Found at i:64162 original size:30 final size:29
Alignment explanation
Indices: 64100--64169 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
64090 ACCGAACCGT
****
64100 CAAATAAGCCCCTAAACTATTATTTCGGC
1 CAAATAAGCCCCTAAACTATTAAAAAGGC
*
64129 CAAATAAGCCCCTAAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTAAACTATT-AAAAAGGC
64159 CAAATAAGCCC
1 CAAATAAGCCC
64170 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTAAACTATTAAAAAGGC
Found at i:70694 original size:22 final size:23
Alignment explanation
Indices: 70644--70692 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
70634 TAATATATAG
* *
70644 TTTTATTTTATTAAAAACTATAT
1 TTTTATTTAATTAAAAACAATAT
**
70667 TTTTATTTAATTAAATTCAATAT
1 TTTTATTTAATTAAAAACAATAT
70690 TTT
1 TTT
70693 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATTTAATTAAAAACAATAT
Found at i:71088 original size:15 final size:16
Alignment explanation
Indices: 71068--71101 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
71058 CACTCAAATG
71068 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
*
71083 TCGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
71099 TCG
1 TCG
71102 TGCCTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:71732 original size:2 final size:2
Alignment explanation
Indices: 71725--71768 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
71715 TAATAATACA
*
71725 AT AT AT AT AT AT AT AT AT AC 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
71767 AT
1 AT
71769 TAAGGAGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.