Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016190.1 Corchorus capsularis cultivar CVL-1 contig16211, 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: 30471
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1177 original size:26 final size:26
Alignment explanation
Indices: 1101--1177 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
1091 TAGCTTACAT
* * * *
1101 ATTATTAATGATGAAAAGCTACTAAA
1 ATTACTAATGATGTAAGGTTACTAAA
* * *
1127 ATTACAACAT-AT-TAAGGTAAATAAA
1 ATTACTA-ATGATGTAAGGTTACTAAA
1152 ATTACTAATGATGTAAGGTTACTAAA
1 ATTACTAATGATGTAAGGTTACTAAA
1178 TTTATGGAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
24 2 0.05
25 16 0.42
26 18 0.47
27 2 0.05
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (26 bp):
ATTACTAATGATGTAAGGTTACTAAA
Found at i:1853 original size:52 final size:49
Alignment explanation
Indices: 1778--1881 Score: 163
Period size: 52 Copynumber: 2.1 Consensus size: 49
1768 AAGATTATAT
*
1778 TTTTTTATGTTATATTACAAATTATTATGCGATTTATTATATTTATTTA
1 TTTTTTATGTTATATTACAAATTAATATGCGATTTATTATATTTATTTA
*
1827 TTTTTTATGATTTATGATTACGAATTAATATGCGATTTATTATATTTATTTA
1 TTTTTTATG--TTAT-ATTACAAATTAATATGCGATTTATTATATTTATTTA
1879 TTT
1 TTT
1882 GTTTTTTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
49 9 0.18
51 4 0.08
52 37 0.74
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.59
Consensus pattern (49 bp):
TTTTTTATGTTATATTACAAATTAATATGCGATTTATTATATTTATTTA
Found at i:1945 original size:2 final size:2
Alignment explanation
Indices: 1938--1963 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1928 CATTAGCTAG
1938 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
1964 CACACACACA
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:2050 original size:22 final size:22
Alignment explanation
Indices: 2009--2052 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1999 TATTCATATG
*
2009 AAATTATGATAATCTTTCTATT
1 AAATTATGATAATCTCTCTATT
2031 AAATTATGATAAT-TACTCTATT
1 AAATTATGATAATCT-CTCTATT
2053 TTTTATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (22 bp):
AAATTATGATAATCTCTCTATT
Found at i:2096 original size:22 final size:22
Alignment explanation
Indices: 2071--2236 Score: 63
Period size: 22 Copynumber: 7.5 Consensus size: 22
2061 TTCCATTATA
2071 AAATTTTGATAACTTTCCTATG
1 AAATTTTGATAACTTTCCTATG
* * *
2093 AAATTTTAATAA-TGATACTATG
1 AAATTTTGATAACT-TTCCTATG
* * *
2115 GAATTTTGAGAACCTTT-TTAT-
1 AAATTTTGATAA-CTTTCCTATG
* ** * *
2136 AAGTTTTTTTTAACCTTCTTATG
1 AA-ATTTTGATAACTTTCCTATG
* * * * *
2159 AAATTTGGTTAACCTCCCTAAG
1 AAATTTTGATAACTTTCCTATG
* * *
2181 GAATTTTGA-AGAC-CTCATTATG
1 AAATTTTGATA-ACTTTC-CTATG
* *
2203 AAATTTTGATAACTTCCCAATG
1 AAATTTTGATAACTTTCCTATG
2225 AAATTTTGATAA
1 AAATTTTGATAA
2237 GCAACACTAT
Statistics
Matches: 102, Mismatches: 32, Indels: 20
0.66 0.21 0.13
Matches are distributed among these distances:
21 7 0.07
22 89 0.87
23 5 0.05
24 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACTTTCCTATG
Found at i:2256 original size:23 final size:22
Alignment explanation
Indices: 2230--2282 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2220 CAATGAAATT
*
2230 TTGATAAGCAACACTATGAGATA
1 TTGATAACCAACA-TATGAGATA
** *
2253 TTGATAACCTCCATATGATATA
1 TTGATAACCAACATATGAGATA
2275 TTGATAAC
1 TTGATAAC
2283 TACGTTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (22 bp):
TTGATAACCAACATATGAGATA
Found at i:2348 original size:22 final size:22
Alignment explanation
Indices: 2323--2563 Score: 95
Period size: 22 Copynumber: 11.1 Consensus size: 22
2313 GAATTGTTAG
*
2323 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
2345 TAATCACAATATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
2367 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
2389 TAAATCTTC-CTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
2412 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** *
2435 TAACTTTC-CTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
2456 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
2473 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * * *
2495 TAACCTCATTATGAATTTTTGT
1 TAATCACACTATGAAATTTTGA
* *
2517 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
2539 T-CTACATACTATGAAATTTTTA
1 TAAT-CACACTATGAAATTTTGA
2561 TAA
1 TAA
2564 CCCTCTTGTC
Statistics
Matches: 167, Mismatches: 39, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.04
17 3 0.02
18 1 0.01
19 2 0.01
21 4 0.02
22 110 0.66
23 38 0.23
24 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:2406 original size:23 final size:23
Alignment explanation
Indices: 2375--2459 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
2365 GATAACCTCG
*
2375 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
2398 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
2421 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* *
2443 CTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
2460 CTACAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 17 0.31
23 37 0.69
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:2444 original size:45 final size:46
Alignment explanation
Indices: 2358--2459 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 46
2348 TCACAATATG
* * *
2358 AAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATA
* *
2403 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTCCTATG
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATA
*
2448 AAATCTTGATAA
1 AAATTTTGATAA
2460 CTACAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 27 0.54
46 23 0.46
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (46 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATA
Found at i:2649 original size:20 final size:20
Alignment explanation
Indices: 2601--2652 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
2591 CTATGAAATT
2601 TTGAAATTTTGATATCCTCA
1 TTGAAATTTTGATATCCTCA
2621 TTG-AATTTTGATATCCTTC-
1 TTGAAATTTTGATATCC-TCA
2640 TTGAAATTTTGAT
1 TTGAAATTTTGAT
2653 TACTCCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (20 bp):
TTGAAATTTTGATATCCTCA
Found at i:2811 original size:22 final size:22
Alignment explanation
Indices: 2761--2925 Score: 86
Period size: 22 Copynumber: 7.6 Consensus size: 22
2751 TCACATTTTG
2761 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* **
2782 GAAATTTTGATAGTCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
2804 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTTTAT
* * * * *
2826 GAAATTATGATAATCACATTAT
1 AAAATTTTGATAACCTCTTTAT
** * *
2848 GTAATTTTAATAACCTCGCTT-T
1 AAAATTTTGATAACCTC-TTTAT
** **
2870 AAAATTTTGATAACAACACTAT
1 AAAATTTTGATAACCTCTTTAT
* *
2892 GAAATTTTGATAA--TCTTTCT
1 AAAATTTTGATAACCTCTTTAT
2912 ATAAATTTTGATAA
1 A-AAATTTTGATAA
2926 TTCTATCTAT
Statistics
Matches: 103, Mismatches: 37, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
20 3 0.03
21 16 0.16
22 82 0.80
23 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.42
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:2854 original size:44 final size:44
Alignment explanation
Indices: 2734--2926 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 44
2724 AGAAATACCA
* * *
2734 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
2778 TTATGAAATTTTGATAGTCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * *
2822 CTATGAAATTATGATAATCACATTATGTAATTTTAATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * **
2866 CTTTAAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCCCT
2910 CTAT-AAATTTTGATAAT
1 CTATGAAATTTTGATAAT
2927 TCTATCTATA
Statistics
Matches: 114, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
43 18 0.16
44 96 0.84
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:3040 original size:22 final size:22
Alignment explanation
Indices: 2871--3065 Score: 77
Period size: 22 Copynumber: 8.7 Consensus size: 22
2861 CCTCGCTTTA
**
2871 AAATTTTGATAA-CAACACTATG
1 AAATTTTGATAACCTTCA-TATG
*
2893 AAATTTTGATAATCTTTC-TAT-
1 AAATTTTGATAA-CCTTCATATG
*
2914 AAATTTTGATAATTCTATCTATATG
1 AAATTTTGATAA-CCT-TC-ATATG
*
2939 AAATTTCGATAATCAC-TC-TATG
1 AAATTTTGATAA-C-CTTCATATG
** *
2961 GGA-TTTGATAACCTTC-TATC
1 AAATTTTGATAACCTTCATATG
* *
2981 AAATTTTGGTACTCCTT-ATGAAATTG
1 AAATTTTGATA-ACCTTCAT---A-TG
*
3007 AGACTTTT-ATAACCTTCATATG
1 A-AATTTTGATAACCTTCATATG
* *
3029 AAATTTTGATAACC-ACACTATA
1 AAATTTTGATAACCTTCA-TATG
3051 AAATTTTGATAACCT
1 AAATTTTGATAACCT
3066 CCCCATGAAA
Statistics
Matches: 131, Mismatches: 22, Indels: 39
0.68 0.11 0.20
Matches are distributed among these distances:
19 1 0.01
20 7 0.05
21 34 0.26
22 53 0.40
23 1 0.01
24 6 0.05
25 17 0.13
26 7 0.05
27 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:3076 original size:22 final size:22
Alignment explanation
Indices: 3026--3076 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3016 TAACCTTCAT
*
3026 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
3048 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
3070 ATGAAAT
1 ATGAAAT
3077 ATTTATTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:3259 original size:22 final size:22
Alignment explanation
Indices: 3229--3336 Score: 103
Period size: 22 Copynumber: 4.9 Consensus size: 22
3219 TAACATGATC
* *
3229 CTATAAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACCATA
* *
3251 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCATA
* *
3273 CTATGGAATTTTGATAA-CATC
1 CTATGAAATTTTGATAACCATA
* *
3294 CTCATGAAATTATAATAACCAT-
1 CT-ATGAAATTTTGATAACCATA
*
3316 CTTATGCAATTTTGATAACCA
1 C-TATGAAATTTTGATAACCA
3337 CATAGAGACA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.06
22 63 0.89
23 4 0.06
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATA
Found at i:11281 original size:19 final size:19
Alignment explanation
Indices: 11257--11295 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11247 TTGCCGCACC
11257 TAACGCAAAGAAACTTATA
1 TAACGCAAAGAAACTTATA
11276 TAACGCAAAGAAACTTATA
1 TAACGCAAAGAAACTTATA
11295 T
1 T
11296 GGAAAAAGGG
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:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (19 bp):
TAACGCAAAGAAACTTATA
Found at i:17547 original size:31 final size:31
Alignment explanation
Indices: 17473--17608 Score: 127
Period size: 31 Copynumber: 4.5 Consensus size: 31
17463 ATCTAACACA
*
17473 AGGCCCTTATTTGAGCATTTTCGATAATGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* *
17504 AGACCATTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* ** * *
17535 AGGCCCTAATTTG-GCCAAATT--A-AAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
* *
17564 GGGCTCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
*
17595 AAGCCCTTATTTGA
1 AGGCCCTTATTTGA
17609 CCAAATTAAA
Statistics
Matches: 79, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
28 3 0.04
29 16 0.20
30 2 0.03
31 55 0.70
32 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:17581 original size:60 final size:60
Alignment explanation
Indices: 17510--17623 Score: 201
Period size: 60 Copynumber: 1.9 Consensus size: 60
17500 TGTTAGACCA
* *
17510 TTATTTGAGCATTTTCGATAACGTTAGGCCCTAATTTGGCCAAATTAAAAGATCGGGCTC
1 TTATTTGAGCATTTTCGATAACGTTAAGCCCTAATTTGACCAAATTAAAAGATCGGGCTC
*
17570 TTATTTGAGCATTTTCGATAACGTTAAGCCCTTATTTGACCAAATTAAAAGATC
1 TTATTTGAGCATTTTCGATAACGTTAAGCCCTAATTTGACCAAATTAAAAGATC
17624 AAATCCTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (60 bp):
TTATTTGAGCATTTTCGATAACGTTAAGCCCTAATTTGACCAAATTAAAAGATCGGGCTC
Found at i:17633 original size:60 final size:60
Alignment explanation
Indices: 17510--17644 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 60
17500 TGTTAGACCA
* * **
17510 TTATTTGAGCATTTTCGATAACGTTAGGCCCTAATTTGGCCAAATTAAAAGATCGGGCTC
1 TTATTTGAGCATTTTCGATAACGTTAAGCCCTAATTTGACCAAATTAAAAGATCAAGCTC
* *
17570 TTATTTGAGCATTTTCGATAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAA-ATCC
1 TTATTTGAGCATTTTCGATAACGTTAAGCCCTAATTTGACCAAATTAAAAGATCAAGCT-C
17630 TTATTTGAGCATTTT
1 TTATTTGAGCATTTT
17645 GACAAATGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 1 0.01
60 67 0.99
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (60 bp):
TTATTTGAGCATTTTCGATAACGTTAAGCCCTAATTTGACCAAATTAAAAGATCAAGCTC
Found at i:17662 original size:60 final size:60
Alignment explanation
Indices: 17510--17668 Score: 198
Period size: 60 Copynumber: 2.6 Consensus size: 60
17500 TGTTAGACCA
* * * **
17510 TTATTTGAGCATTTTCGATAACGTTAGGCCCTAATTTGGCCAAATTAAAAGATCGGGCTC
1 TTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGACCAAATTAAAAGATCAAGCTC
*
17570 TTATTTGAGCATTTTCGATAACGTTA-AGCCCTTATTTGACCAAATTAAAAGATCAA-ATCC
1 TTATTTGAGCATTTTCGATAACGTTAGA-CCCTTATTTGACCAAATTAAAAGATCAAGCT-C
* *
17630 TTATTTGAGCATTTT-GACAAATGTTAGACCCTTATTTGA
1 TTATTTGAGCATTTTCGA-TAACGTTAGACCCTTATTTGA
17669 GCAATTAGCC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 3 0.03
60 83 0.95
61 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
TTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGACCAAATTAAAAGATCAAGCTC
Found at i:18686 original size:14 final size:14
Alignment explanation
Indices: 18667--18737 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
18657 TTTATTTTAT
18667 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
18681 AAATTCAGTTAAG-
1 AAATTCTTTTAAGA
* * *
18694 AAATTTTATTTTA-T
1 AAATTCT-TTTAAGA
18708 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
18722 AAATTCAGTTAAGA
1 AAATTCTTTTAAGA
18736 AA
1 AA
18738 TGAAATTTTA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
13 9 0.21
14 34 0.79
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATTCTTTTAAGA
Found at i:18713 original size:41 final size:41
Alignment explanation
Indices: 18656--18738 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
18646 CGTGCGACTG
18656 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
18697 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
18738 T
1 T
18739 GAAATTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (41 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Found at i:18746 original size:41 final size:41
Alignment explanation
Indices: 18660--18748 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
18650 CGACTGTTTT
***
18660 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATTTT
1 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAA
18701 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAA
1 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAA
18742 ATTTTAT
1 ATTTTAT
18749 TGTGAAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (41 bp):
ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAA
Found at i:19065 original size:11 final size:11
Alignment explanation
Indices: 19051--19088 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19041 ATTCATAACA
19051 AATTTATAATT
1 AATTTATAATT
19062 AATTTATAATT
1 AATTTATAATT
19073 -ATTTGATAATT
1 AATTT-ATAATT
*
19084 TATTT
1 AATTT
19089 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:20241 original size:2 final size:2
Alignment explanation
Indices: 20234--20268 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20224 AAAACTATTC
20234 AT AT 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 AT AT A
20269 CTACATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23291 original size:33 final size:32
Alignment explanation
Indices: 23249--23310 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
23239 CAATACAAAG
23249 TACAATGAACTATTGGATTTAAAGGAAAAAAAA
1 TACAATGAACTATTGGATTTAAA-GAAAAAAAA
*
23282 TACAATGAACTATTGGGTTTAAAGAAAAA
1 TACAATGAACTATTGGATTTAAAGAAAAA
23311 TACAAGCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (32 bp):
TACAATGAACTATTGGATTTAAAGAAAAAAAA
Found at i:23465 original size:60 final size:60
Alignment explanation
Indices: 23372--23493 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
23362 ATAAACACAC
23372 ATACCAAACAATACAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCAAA
1 ATACCAAACAATACAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCAAA
*
23432 ATACCAAACAATACAAAGTGCAATGAACTATTGGATTTAAAGAAAATTACAAGCACCAAA
1 ATACCAAACAATACAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCAAA
23492 AT
1 AT
23494 GATTATAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.20
Consensus pattern (60 bp):
ATACCAAACAATACAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCAAA
Found at i:30148 original size:39 final size:39
Alignment explanation
Indices: 30094--30172 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
30084 TCGGAAAGAC
* *
30094 TTGTAAAAGAGATCATCAATTATAGGTCGAATCAAAAAT
1 TTGTAAAAGAGATCATCAATTAAAGGTCCAATCAAAAAT
* * *
30133 TTGTAAAAGATATCATCAATTAAATGTCCAATTAAAAAT
1 TTGTAAAAGAGATCATCAATTAAAGGTCCAATCAAAAAT
30172 T
1 T
30173 CAGTCGCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (39 bp):
TTGTAAAAGAGATCATCAATTAAAGGTCCAATCAAAAAT
Done.