Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold624
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: 16271
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.23
Warning! 4510 characters in sequence are not A, C, G, or T
Found at i:1937 original size:21 final size:19
Alignment explanation
Indices: 1911--1949 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1901 TCAACCATTC
1911 AAAACACAATCAAATACAATT
1 AAAACA-AATCAAA-ACAATT
*
1932 AAAACATATCAAAACAAT
1 AAAACAAATCAAAACAAT
1950 AATCATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAACAAATCAAAACAATT
Found at i:2486 original size:21 final size:20
Alignment explanation
Indices: 2462--2512 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
2452 ATTCATAACA
*
2462 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
2483 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTGC
*
2504 TATACAAAT
1 TATTCAAAT
2513 AGCTTTCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:2489 original size:22 final size:21
Alignment explanation
Indices: 2464--2506 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2454 TCATAACATA
*
2464 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
2486 TTCAAATCTCATACTTGCTAT
1 TTCAAATCTCATACTTGCTAT
2507 ACAAATAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:2793 original size:41 final size:40
Alignment explanation
Indices: 2683--2803 Score: 128
Period size: 37 Copynumber: 3.1 Consensus size: 40
2673 CCCAGTACCA
*
2683 CATCAGA-TAATTCGAAGTAATAAATTGAAACCCAGTGTCT
1 CATCAGATTAA-TCGAAGTAATAAATTGACACCCAGTGTCT
* * *
2723 CATCAGCTAAATCG--G-AATAAATTGGCACCCAGTG-CGT
1 CATCAGATTAATCGAAGTAATAAATTGACACCCAGTGTC-T
2760 CATC-GAATTAATCCGAAGTAATAAATTGACACCCAGTGTCT
1 CATCAG-ATTAAT-CGAAGTAATAAATTGACACCCAGTGTCT
2801 CAT
1 CAT
2804 TGACTCGAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
36 2 0.03
37 26 0.39
38 3 0.05
40 10 0.15
41 24 0.36
42 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (40 bp):
CATCAGATTAATCGAAGTAATAAATTGACACCCAGTGTCT
Found at i:3670 original size:4 final size:4
Alignment explanation
Indices: 3661--3747 Score: 70
Period size: 4 Copynumber: 21.2 Consensus size: 4
3651 ACTTTTCTCC
* * *
3661 TTCT TTCT TTCT TTTT TTCT TTCCT TTCT TTCT TTCT CTGT TTCGT TTCT
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTC-T TTCT
* * *
3711 TTCT CTCC TTCT TT-T TCTCA TTCT TT-T TCTCT TTCT T
1 TTCT TTCT TTCT TTCT T-TCT TTCT TTCT T-TCT TTCT T
3748 AATTATTTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
3 4 0.06
4 50 0.77
5 11 0.17
ACGTcount: A:0.01, C:0.26, G:0.02, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:3677 original size:21 final size:21
Alignment explanation
Indices: 3653--3695 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3643 AAACCCTAAC
*
3653 TTTTCTCCTT-CTTTCTTTCT
1 TTTTTTCCTTCCTTTCTTTCT
*
3673 TTTTTTCTTTCCTTTCTTTCT
1 TTTTTTCCTTCCTTTCTTTCT
3694 TT
1 TT
3696 CTCTGTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTCCTTCCTTTCTTTCT
Found at i:3691 original size:25 final size:24
Alignment explanation
Indices: 3661--3747 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
3651 ACTTTTCTCC
3661 TTCTTTCTTTCTTTTTTTCTTTCCT
1 TTCTTTCTTTCTTTTTTTCTTT-CT
* *
3686 TTCTTTCTTTCTCTGTTTCGTTTCT
1 TTCTTTCTTTCTTTTTTTC-TTTCT
* * * *
3711 TTCTCTCCTTCTTTTTCTCATTCT
1 TTCTTTCTTTCTTTTTTTCTTTCT
3735 TT-TTCTCTTTCTT
1 TTCTT-TCTTTCTT
3748 AATTATTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.02
24 13 0.26
25 33 0.66
26 3 0.06
ACGTcount: A:0.01, C:0.26, G:0.02, T:0.70
Consensus pattern (24 bp):
TTCTTTCTTTCTTTTTTTCTTTCT
Found at i:3704 original size:21 final size:21
Alignment explanation
Indices: 3663--3714 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3653 TTTTCTCCTT
* *
3663 CTTTCTTTCTTTTTTTCTTTC
1 CTTTCTTTCTTTCTCTCTTTC
*
3684 CTTTCTTTCTTTCTCTGTTTC
1 CTTTCTTTCTTTCTCTCTTTC
*
3705 GTTTCTTTCT
1 CTTTCTTTCT
3715 CTCCTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (21 bp):
CTTTCTTTCTTTCTCTCTTTC
Found at i:3709 original size:17 final size:16
Alignment explanation
Indices: 3685--3716 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3675 TTTTCTTTCC
3685 TTTCTTTCTTTCTCTG
1 TTTCTTTCTTTCTCTG
3701 TTTCGTTTCTTTCTCT
1 TTTC-TTTCTTTCTCT
3717 CCTTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTCTTTCTTTCTCTG
Found at i:3803 original size:37 final size:38
Alignment explanation
Indices: 3753--3838 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
3743 TTCTTAATTA
*
3753 TTTTAATATAATATAAT-ATATATA-ATTAATATTTAAG
1 TTTTATTATAATATAATAATATATATATTAA-ATTTAAG
* * *
3790 TTTTATTATAATATTATAATATATATTTTAACTTTAAG
1 TTTTATTATAATATAATAATATATATATTAAATTTAAG
*
3828 TTTTATAATAA
1 TTTTATTATAA
3839 AATACACTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 15 0.36
38 23 0.55
39 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (38 bp):
TTTTATTATAATATAATAATATATATATTAAATTTAAG
Found at i:5816 original size:27 final size:25
Alignment explanation
Indices: 5776--5861 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
5766 AATGCTCATA
*
5776 CGAGCACATA-AACGGGAAGCACTTTCT
1 CGAGC-CATATAACGGGAAGCAC-AT-T
*
5803 CGAGCCATATAACGGGAAGCTCATT
1 CGAGCCATATAACGGGAAGCACATT
** * *
5828 CGAGCTGTATAACGGGAAGCTCATA
1 CGAGCCATATAACGGGAAGCACATT
*
5853 AGAGCCATA
1 CGAGCCATA
5862 ATCAGGAAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 29 0.58
26 5 0.10
27 16 0.32
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCACATT
Found at i:5857 original size:25 final size:25
Alignment explanation
Indices: 5810--5857 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5800 TCTCGAGCCA
**
5810 TATAACGGGAAGCTCATTCGAGCTG
1 TATAACGGGAAGCTCATAAGAGCTG
5835 TATAACGGGAAGCTCATAAGAGC
1 TATAACGGGAAGCTCATAAGAGC
5858 CATAATCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (25 bp):
TATAACGGGAAGCTCATAAGAGCTG
Found at i:6128 original size:24 final size:25
Alignment explanation
Indices: 6062--6128 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
6052 CTAGCAAGAA
*
6062 CCATATAAC-AGGAAGCTCATGAGAG
1 CCATATAACGA-GACGCTCATGAGAG
* *
6087 CCATATATCGAGATGCTCATGAGAG
1 CCATATAACGAGACGCTCATGAGAG
**
6112 GTA-ATAACGAGACGCTC
1 CCATATAACGAGACGCTC
6129 TTTCAAGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 12 0.34
25 22 0.63
26 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
CCATATAACGAGACGCTCATGAGAG
Found at i:9296 original size:125 final size:125
Alignment explanation
Indices: 9153--9984 Score: 1612
Period size: 125 Copynumber: 6.7 Consensus size: 125
9143 GCTTACAGAA
* * * *
9153 AAAAATGCCGTTAAAGATCATGTTCTTTAGCGGCGC-TAAGGAAATAAACGCCGCTAAAGATCAT
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAA-GAAAAAAACGCCGCTAAAGATCAT
9217 GTTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
65 GTTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
9278 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
9343 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
66 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
9403 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
9468 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
66 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
9528 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
9593 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
66 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
9653 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
9718 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
66 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
9778 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
9843 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
66 TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
9903 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
9968 TTCTTTAGCGGCGCTTA
66 TTCTTTAGCGGCGCTTA
9985 NNNNNNNNNN
Statistics
Matches: 702, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
125 699 1.00
126 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (125 bp):
AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTTATGAAAAACGCTGCTACAGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:15909 original size:9 final size:9
Alignment explanation
Indices: 15892--16013 Score: 80
Period size: 9 Copynumber: 14.4 Consensus size: 9
15882 AATTTATGTA
*
15892 TTATATAAG
1 TTATGTAAG
15901 TTATGTAAG
1 TTATGTAAG
*
15910 TTACGT-A-
1 TTATGTAAG
15917 TTATGTAAG
1 TTATGTAAG
*
15926 CTATGTAAG
1 TTATGTAAG
**
15935 -T-TGTATT
1 TTATGTAAG
*
15942 TTATGTTAG
1 TTATGTAAG
* *
15951 CTAT-TTA-
1 TTATGTAAG
15958 TTATGTAAG
1 TTATGTAAG
*
15967 CTATGTAAG
1 TTATGTAAG
*
15976 TTGTGT-A-
1 TTATGTAAG
15983 TTATGTAAG
1 TTATGTAAG
*
15992 CTATGTAAG
1 TTATGTAAG
*
16001 TTATGTGAG
1 TTATGTAAG
16010 TTAT
1 TTAT
16014 ATATAAGTTA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
7 17 0.20
8 11 0.13
9 58 0.67
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:15925 original size:25 final size:23
Alignment explanation
Indices: 15888--16002 Score: 107
Period size: 25 Copynumber: 5.0 Consensus size: 23
15878 TGAAAATTTA
* *
15888 TGTATTATATAAGTTATGTAAGT
1 TGTATTATGTAAGCTATGTAAGT
15911 TACGTATTATGTAAGCTATGTAAGT
1 T--GTATTATGTAAGCTATGTAAGT
* *
15936 TGTATT-T-TATGTTA-GCT-A-T
1 TGTATTATGTAAGCTATG-TAAGT
15955 T-TATTATGTAAGCTATGTAAGTT
1 TGTATTATGTAAGCTATGTAAG-T
15978 GTGTATTATGTAAGCTATGTAAGT
1 -TGTATTATGTAAGCTATGTAAGT
16002 T
1 T
16003 ATGTGAGTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.05
19 3 0.04
20 8 0.11
21 8 0.11
22 1 0.01
23 8 0.11
24 2 0.03
25 41 0.55
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (23 bp):
TGTATTATGTAAGCTATGTAAGT
Found at i:15995 original size:41 final size:41
Alignment explanation
Indices: 15901--15998 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
15891 ATTATATAAG
* * *
15901 TTATGTAAGTTACGTATTATGTAAGCTATGTAAGTTGTATT
1 TTATGTAAGCTATGTATTATGTAAGCTATGTAAGTTGTATA
* * *
15942 TTATGTTAGCTATTTATTATGTAAGCTATGTAAGTTGTGTA
1 TTATGTAAGCTATGTATTATGTAAGCTATGTAAGTTGTATA
15983 TTATGTAAGCTATGTA
1 TTATGTAAGCTATGTA
15999 AGTTATGTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (41 bp):
TTATGTAAGCTATGTATTATGTAAGCTATGTAAGTTGTATA
Found at i:16039 original size:21 final size:21
Alignment explanation
Indices: 16013--16062 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
16003 ATGTGAGTTA
16013 TATATAAGTTATCTTAATAAT
1 TATATAAGTTATCTTAATAAT
16034 TATATAAGTTATCTTAATAAT
1 TATATAAGTTATCTTAATAAT
16055 TATATAAG
1 TATATAAG
16063 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAAGTTATCTTAATAAT
Found at i:16147 original size:34 final size:32
Alignment explanation
Indices: 16108--16196 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 32
16098 AAGTAATGTA
16108 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAG
1 TTATGTAAGTTGTGTATAATGTTAGTTAT--AAG
*
16142 TTATGT-A-TTATG--TAA-GTTA-TT-TAAG
1 TTATGTAAGTTGTGTATAATGTTAGTTATAAG
* *
16167 TTATGTAAGTTGTGTATTATGTAAGTTATA
1 TTATGTAAGTTGTGTATAATGTTAGTTATA
16197 TAGGCTATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
25 9 0.20
26 1 0.02
27 5 0.11
28 2 0.05
29 6 0.14
30 6 0.14
31 2 0.05
32 6 0.14
33 1 0.02
34 6 0.14
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.48
Consensus pattern (32 bp):
TTATGTAAGTTGTGTATAATGTTAGTTATAAG
Found at i:16161 original size:9 final size:9
Alignment explanation
Indices: 16091--16247 Score: 84
Period size: 9 Copynumber: 18.3 Consensus size: 9
16081 NNNNNNGTAT
*
16091 GTTAAGTAA
1 GTTATGTAA
*
16100 GTAATGT-A
1 GTTATGTAA
16108 -TTATGTAA
1 GTTATGTAA
*
16116 GTTGTGT-A
1 GTTATGTAA
* *
16124 -TAATGTTA
1 GTTATGTAA
**
16132 GTTATCAAA
1 GTTATGTAA
16141 GTTATGT-A
1 GTTATGTAA
16149 -TTATGTAA
1 GTTATGTAA
*
16157 GTTATTTAA
1 GTTATGTAA
16166 GTTATGTAA
1 GTTATGTAA
*
16175 GTTGTGT-A
1 GTTATGTAA
16183 -TTATGTAA
1 GTTATGTAA
* *
16191 GTTATATAG
1 GTTATGTAA
*
16200 GCTATGT-A
1 GTTATGTAA
16208 -TTATGTAA
1 GTTATGTAA
*
16216 GTTAT-TAT
1 GTTATGTAA
16224 GCTATTATGTAA
1 G---TTATGTAA
*
16236 GTTATGCAA
1 GTTATGTAA
16245 GTT
1 GTT
16248 TATATATAAG
Statistics
Matches: 109, Mismatches: 25, Indels: 28
0.67 0.15 0.17
Matches are distributed among these distances:
7 25 0.23
8 12 0.11
9 65 0.60
11 4 0.04
12 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.46
Consensus pattern (9 bp):
GTTATGTAA
Found at i:16176 original size:59 final size:59
Alignment explanation
Indices: 16108--16221 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
16098 AAGTAATGTA
* *
16108 TTATGTAAGTTGTGTATAATGTTAGTTATCA-AAGTTATGTATTATGTAAGTTATTTAAG
1 TTATGTAAGTTGTGTATAATGTAAGTTAT-ATAAGCTATGTATTATGTAAGTTATTTAAG
* *
16167 TTATGTAAGTTGTGTATTATGTAAGTTATATAGGCTATGTATTATGTAAGTTATT
1 TTATGTAAGTTGTGTATAATGTAAGTTATATAAGCTATGTATTATGTAAGTTATT
16222 ATGCTATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 1 0.02
59 49 0.98
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (59 bp):
TTATGTAAGTTGTGTATAATGTAAGTTATATAAGCTATGTATTATGTAAGTTATTTAAG
Found at i:16186 original size:25 final size:25
Alignment explanation
Indices: 16158--16228 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
16148 ATTATGTAAG
* * * *
16158 TTATTTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATATAAGCTATGTA
*
16183 TTATGTAAGTTATATAGGCTATGTA
1 TTATGTAAGTTATATAAGCTATGTA
*
16208 TTATGTAAGTTAT-TATGCTAT
1 TTATGTAAGTTATATAAGCTAT
16229 TATGTAAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 7 0.17
25 33 0.82
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.49
Consensus pattern (25 bp):
TTATGTAAGTTATATAAGCTATGTA
Found at i:16206 original size:34 final size:34
Alignment explanation
Indices: 16139--16214 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
16129 TTAGTTATCA
* *
16139 AAGTTATGTATTATGTAAGTTATTTAAGTTATGT
1 AAGTTATGTATTATGTAAGTTATATAAGCTATGT
* *
16173 AAGTTGTGTATTATGTAAGTTATATAGGCTATGT
1 AAGTTATGTATTATGTAAGTTATATAAGCTATGT
16207 -A-TTATGTA
1 AAGTTATGTA
16215 AGTTATTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 6 0.16
33 1 0.03
34 30 0.81
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (34 bp):
AAGTTATGTATTATGTAAGTTATATAAGCTATGT
Found at i:16231 original size:20 final size:19
Alignment explanation
Indices: 16142--16240 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 19
16132 GTTATCAAAG
16142 TTATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
*
16161 TT-T-AAGTTATGTAAG---
1 TTATGTA-TTATGTAAGTTA
*
16176 TTGTGTATTATGTAAGTTATA
1 TTATGTATTATGTAAG-T-TA
16197 TAGGCTATGTATTATGTAAGTTA
1 T----TATGTATTATGTAAGTTA
16220 TTATGCTATTATGTAAGTTA
1 TTATG-TATTATGTAAGTTA
16240 T
1 T
16241 GCAAGTTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
15 2 0.03
16 10 0.16
17 2 0.03
18 10 0.16
19 6 0.09
20 15 0.23
21 1 0.02
23 3 0.05
24 1 0.02
25 14 0.22
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.49
Consensus pattern (19 bp):
TTATGTATTATGTAAGTTA
Done.