Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006699.1 Corchorus capsularis cultivar CVL-1 contig06720, 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: 28488
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3790 original size:28 final size:28
Alignment explanation
Indices: 3759--3815 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3749 AGAAGGTAAA
3759 AAAATCTGAATTCATTTTCAGAAAATTT
1 AAAATCTGAATTCATTTTCAGAAAATTT
3787 AAAATCTGAATTCATTTTCAGAAAATTT
1 AAAATCTGAATTCATTTTCAGAAAATTT
3815 A
1 A
3816 TTTTTGGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (28 bp):
AAAATCTGAATTCATTTTCAGAAAATTT
Found at i:8528 original size:31 final size:31
Alignment explanation
Indices: 8490--8551 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
8480 AGTTTTGTAA
8490 AACTTTTGAAACGCCTATTATACCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
* *
8521 AACTTTTGAAACGTCTATTATATCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
8552 GTCTAACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATTT
Found at i:9573 original size:7 final size:7
Alignment explanation
Indices: 9561--9585 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9551 CCAAAGGCTT
9561 GAATGCA
1 GAATGCA
9568 GAATGCA
1 GAATGCA
9575 GAATGCA
1 GAATGCA
9582 GAAT
1 GAAT
9586 TCTTGCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.16
Consensus pattern (7 bp):
GAATGCA
Found at i:10389 original size:14 final size:14
Alignment explanation
Indices: 10370--10398 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10360 AAAATTTTGC
10370 TTTTGAGTCCTTCA
1 TTTTGAGTCCTTCA
10384 TTTTGAGTCCTTCA
1 TTTTGAGTCCTTCA
10398 T
1 T
10399 GAAAGTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTTGAGTCCTTCA
Found at i:12301 original size:24 final size:24
Alignment explanation
Indices: 12274--12321 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
12264 TCTTTGGTGT
12274 TGGCCATTGCAAAATGCATTTGAC
1 TGGCCATTGCAAAATGCATTTGAC
*
12298 TGGCCATTGTAAAATGCATTTGAC
1 TGGCCATTGCAAAATGCATTTGAC
12322 CTTTCCATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (24 bp):
TGGCCATTGCAAAATGCATTTGAC
Found at i:15047 original size:21 final size:18
Alignment explanation
Indices: 15009--15049 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
14999 GGAATATTCT
15009 TGCTTCCAATGACTTCAA
1 TGCTTCCAATGACTTCAA
15027 TGCTCTCCAATTGATCTTCAA
1 TGCT-TCCAA-TGA-CTTCAA
15048 TG
1 TG
15050 GTCTTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 3 0.15
21 8 0.40
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTTCCAATGACTTCAA
Found at i:17471 original size:37 final size:37
Alignment explanation
Indices: 17423--18607 Score: 948
Period size: 37 Copynumber: 32.1 Consensus size: 37
17413 CAGTCTCGTC
*
17423 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTTTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
17461 AAATCTTGTTTAAGATTCATGTTTAGGT-TTCTTATC-
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* * * *
17497 AAATCCTTATTTAAGGTCTCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* *
17535 AAATCTTGTTTAAGATTCCTGTTTAGGT-TTCTTATC-
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* *
17571 AAATCCTTG-TTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * * *
17608 AAATCTTCTTTAAGATTCCTGTTTAGGT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* * *
17644 AAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
17682 AAATCTTGTTTAAGATTCCTGTTTAGGT-TTCTTAT-G
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
*
17718 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTTTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
17756 AAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTTATC-
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGT-TTCATCA
* * * * * *
17793 AAATCCTCGTTTAAGGTCCTTGTTTAGGTATCTCATCT
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* ** *
17831 AAATTTTGTTTAAGATTACTGTTTAGGT-TTCTTATC-
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
*
17867 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATC-
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
17904 AAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * * *
17942 AAATTTTGTTTAAGATTCCTGTTTAGGT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* *
17978 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
18016 AAATCTTGTTTAAGATTCC----TAGGT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* *
18048 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * * *
18086 AAATCTTGTTTAAGATTCATGTTTAGGT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* * * *
18122 AAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTCGTCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * * *
18160 AAATCTTGTTTAAGATTCCTGTTTAGAT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* * *
18196 AAATCCTTGTTTAAGCTCTCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * * * *
18234 AAATCTTGTTTAAAATTCATGTTTAGGT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
*
18270 AAATCTTTGTTTAAGGTCCCTGTTTAGGTGTTTCATCA
1 AAATC-TTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * * *
18308 AAATCTTGTTTAAGTTTCCC-GTTTAGAT-TTCTTAT-T
1 AAATCTTGTTTAAG-ATCCCTGTTTAGGTGTT-TCATCA
* * *
18344 AAATCATTGTTTAAGGTCCCTGTTTAGGTGTCTCAACA
1 AAATC-TTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
18382 AAATCTTGTTTAAGATTCTTGTTTAGGT-TTCTTATC-
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* *
18418 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* *
18456 AAATCTTGTTTAAGATTCCTGTTTAGGT-TTCTTAT-A
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* * * * *
18492 TAATCATTATTTAAGGTCCATGTTTAGGTGTCTCATCA
1 AAATC-TTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
* * *
18530 AAATCTTGTTCAAGATCCCTGTTTAGGT-TTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTT-TCATCA
* * *
18566 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCACCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
18604 AAAT
1 AAAT
18608 TTTATGAAAT
Statistics
Matches: 899, Mismatches: 182, Indels: 132
0.74 0.15 0.11
Matches are distributed among these distances:
32 5 0.01
33 21 0.02
36 98 0.11
37 667 0.74
38 108 0.12
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.45
Consensus pattern (37 bp):
AAATCTTGTTTAAGATCCCTGTTTAGGTGTTTCATCA
Found at i:18595 original size:74 final size:74
Alignment explanation
Indices: 17415--18607 Score: 1260
Period size: 74 Copynumber: 16.2 Consensus size: 74
17405 CCAAAATTCA
* * * * *
17415 GTCTCGTC-AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTTAAGAT
1 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGT-TTCTTAT-TAAATCCTTGTTTAAGGT
* *
17477 TCATGTTTAGGT
63 CCCTGTTTAGGT
* * * * * * * * * *
17489 TTCTTATC-AAATCCTTATTTAAGGTCTCTGTTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATT
1 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGTTTCTTAT-TAAATCCTTGTTTAAGGTC
17552 CCTGTTTAGGT
64 CCTGTTTAGGT
* * * * * * * * *
17563 TTCTTATC-AAATCCTTG-TTAAGGTCCCTGTTTAGGTGTCTCATCAAAAT-CTTCTTTAAGATT
1 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGTTTCTTAT-TAAATCCTTGTTTAAGGTC
17625 CCTGTTTAGGT
64 CCTGTTTAGGT
* * * * * * * * * *
17636 TTCTTAT-TAAATCCTTGTTTAAGGTCCCTATTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATT
1 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGTTTCTTAT-TAAATCCTTGTTTAAGGTC
17699 CCTGTTTAGGT
64 CCTGTTTAGGT
* * * * * * *
17710 TTCTTAT-GAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTTAAGAT
1 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGT-TTCTTAT-TAAATCCTTGTTTAAGGT
*
17772 TCCTGTTTAGGT
63 CCCTGTTTAGGT
* * * * * * * * *
17784 TTCTTTATC-AAATCCTCGTTTAAGGTCCTTGTTTAGGTATCTCATCTAAAT-TTTGTTTAAGAT
1 GTC-TCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGTTTCTTAT-TAAATCCTTGTTTAAGGT
**
17847 TACTGTTTAGGT
63 CCCTGTTTAGGT
* * * * *
17859 TTCTTATC-AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCAAATCCTTGTTTAAGGTCC
1 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCC
*
17923 CTATTTAGGT
65 CTGTTTAGGT
* *
17933 GTCTCATCAAAATTTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
17998 TGTTTAGGT
66 TGTTTAGGT
*
18007 GTCTCATCAAAATCTTGTTTAAGATTCC----TAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
18068 TGTTTAGGT
66 TGTTTAGGT
* *
18077 GTCTCATCAAAATCTTGTTTAAGATTCATGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
*
18142 TATTTAGGT
66 TGTTTAGGT
* * * * *
18151 GTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGATTTCTTATTAAATCCTTGTTTAAGCTCTC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
18216 TGTTTAGGT
66 TGTTTAGGT
* * * *
18225 GTCTCATCAAAATCTTGTTTAAAATTCATGTTTAGGTTTCTTATTAAATCTTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
18290 TGTTTAGGT
66 TGTTTAGGT
* * * *
18299 GTTTCATCAAAATCTTGTTTAAGTTTCCC-GTTTAGATTTCTTATTAAATCATTGTTTAAGGTCC
1 GTCTCATCAAAATCTTGTTTAAG-ATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCC
18363 CTGTTTAGGT
65 CTGTTTAGGT
* * * *
18373 GTCTCAACAAAATCTTGTTTAAGATTCTTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
18438 TGTTTAGGT
66 TGTTTAGGT
* * *
18447 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTA-TATAATCATTATTTAAGGTCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTA-AATCCTTGTTTAAGGTCC
*
18511 ATGTTTAGGT
65 CTGTTTAGGT
*
18521 GTCTCATCAAAATCTTGTTCAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
18586 TGTTTAGGT
66 TGTTTAGGT
*
18595 GTCTCACCAAAAT
1 GTCTCATCAAAAT
18608 TTTATGAAAT
Statistics
Matches: 1020, Mismatches: 82, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
70 69 0.07
73 78 0.08
74 799 0.78
75 74 0.07
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
TGTTTAGGT
Found at i:18799 original size:14 final size:14
Alignment explanation
Indices: 18780--18807 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18770 TGCATTTTAT
18780 TTCAAAACTCAAAA
1 TTCAAAACTCAAAA
18794 TTCAAAACTCAAAA
1 TTCAAAACTCAAAA
18808 CACGCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
TTCAAAACTCAAAA
Found at i:18994 original size:7 final size:7
Alignment explanation
Indices: 18982--19016 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
18972 TGGTGTATTC
18982 TTCAAAA
1 TTCAAAA
18989 TTCAAAA
1 TTCAAAA
18996 TTCAAAA
1 TTCAAAA
19003 TTCAAAA
1 TTCAAAA
19010 TTCAAAA
1 TTCAAAA
19017 CTTGCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (7 bp):
TTCAAAA
Found at i:19113 original size:35 final size:35
Alignment explanation
Indices: 19043--19122 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
19033 CCATTCTTCG
** *
19043 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
1 AAAATCAAAATTCAAAATCAGCATTTCATGATTCA
* *
19078 AAAATTAAAATTCAAAATCAGCATCTT-ATGGTTCA
1 AAAATCAAAATTCAAAATCAGCAT-TTCATGATTCA
*
19113 AAATTCAAAA
1 AAAATCAAAA
19123 CCTGCATTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (35 bp):
AAAATCAAAATTCAAAATCAGCATTTCATGATTCA
Found at i:19115 original size:28 final size:28
Alignment explanation
Indices: 19084--19140 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
19074 TTCAAAAATT
*
19084 AAAATTCAAAATCAGCATCTT-ATGGTTC
1 AAAATTCAAAACCAGCAT-TTCATGGTTC
*
19112 AAAATTCAAAACCTGCATTTCATGGTTC
1 AAAATTCAAAACCAGCATTTCATGGTTC
19140 A
1 A
19141 TTCTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (28 bp):
AAAATTCAAAACCAGCATTTCATGGTTC
Found at i:24709 original size:2 final size:2
Alignment explanation
Indices: 24702--24743 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
24692 CTTCTCGTCA
24702 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
24744 CCACCAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24873 original size:2 final size:2
Alignment explanation
Indices: 24866--24893 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24856 CATAATAATA
24866 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
24894 GACTATATTC
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:28131 original size:22 final size:22
Alignment explanation
Indices: 28106--28477 Score: 82
Period size: 22 Copynumber: 16.8 Consensus size: 22
28096 ATGATCCCAT
28106 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** **
28128 TATGAAATTTTAATAACGATAT
1 TATGAAATTTTGATAACCTTCC
* * * * **
28150 TATGGAATTTCGAAAATCTTTT
1 TATGAAATTTTGATAACCTTCC
** * *
28172 TAT-AAATTTTTTTTAACGTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
28194 TATTAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
28216 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
* *
28238 TATGAAATTTTAATAACTTTCC
1 TATGAAATTTTGATAACCTTCC
* * **
28260 AATGAAATTTTAATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
28283 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
28304 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
28327 TATGAAAATTT-AAAAACTTACA
1 TATGAAATTTTGATAACCTT-CC
* *
28349 TATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATT-TTGA-TAACCTTC-C
* * * *
28371 TCTGAAATATTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
28393 TATGAAATTGTAATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
* *
28415 TATGAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* *
28438 TATAAAATTTTGATAAACCTTTC
1 TATGAAATTTTGAT-AACCTTCC
*
28461 TATAAAATTTTGATAAC
1 TATGAAATTTTGATAAC
28478 TTTCTTATTA
Statistics
Matches: 252, Mismatches: 80, Indels: 36
0.68 0.22 0.10
Matches are distributed among these distances:
21 13 0.05
22 173 0.69
23 65 0.26
24 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:28153 original size:44 final size:44
Alignment explanation
Indices: 28104--28276 Score: 109
Period size: 44 Copynumber: 3.9 Consensus size: 44
28094 TAATGATCCC
28104 ATTATGAAATTTTGATAACCTTCCTATGAAATTTTAATAACGAT
1 ATTATGAAATTTTGATAACCTTCCTATGAAATTTTAATAACGAT
* * * * ** ** *
28148 ATTATGGAATTTCGAAAATCTTTTTAT-AAATTTTTTTTAACGTT
1 ATTATGAAATTTTGATAACCTTCCTATGAAA-TTTTAATAACGAT
* * * * * * * *
28192 CTTATTAAATTTTGTTAACCTCCCTAAGGAATTTTGAA-GAC-CT
1 ATTATGAAATTTTGATAACCTTCCTATGAAATTTT-AATAACGAT
* * * *
28235 CAATATGAAATTTTAATAACTTTCCAATGAAATTTTAATAAC
1 -ATTATGAAATTTTGATAACCTTCCTATGAAATTTTAATAAC
28277 CAACACTATG
Statistics
Matches: 88, Mismatches: 36, Indels: 10
0.66 0.27 0.07
Matches are distributed among these distances:
43 6 0.07
44 80 0.91
45 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (44 bp):
ATTATGAAATTTTGATAACCTTCCTATGAAATTTTAATAACGAT
Found at i:28445 original size:23 final size:23
Alignment explanation
Indices: 28419--28476 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
28409 CCTCGTTATG
*
28419 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
**
28442 AAATTTTGATAAACCTTTCTATA
1 AAATTTTGATAAACCTCCCTATA
28465 AAATTTTGATAA
1 AAATTTTGATAA
28477 CTTTCTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Done.