Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014934.1 Corchorus capsularis cultivar CVL-1 contig14955, 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: 45869
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1684 original size:21 final size:22
Alignment explanation
Indices: 1657--1715 Score: 93
Period size: 21 Copynumber: 2.7 Consensus size: 22
1647 AAAATATTCA
1657 TATGAAGTTATGATAACCTCTC
1 TATGAAGTTATGATAACCTCTC
1679 TA-GAAGTTATGATAACCTCTC
1 TATGAAGTTATGATAACCTCTC
* *
1700 TATTAAATTATGATAA
1 TATGAAGTTATGATAA
1716 TTACACTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAGTTATGATAACCTCTC
Found at i:1765 original size:22 final size:22
Alignment explanation
Indices: 1740--1836 Score: 70
Period size: 22 Copynumber: 4.4 Consensus size: 22
1730 ATGACCCCAT
1740 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTTC
* ****
1762 TATGAAATTTTAATAACGACAC
1 TATGAAATTTTGATAACCTTTC
* * * *
1784 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTTC
** *
1806 TAT-AAATTTTTCTTAACCTTTT
1 TATGAAA-TTTTGATAACCTTTC
1828 TATGAAATT
1 TATGAAATT
1837 CGGTTAACCT
Statistics
Matches: 54, Mismatches: 19, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
21 2 0.04
22 49 0.91
23 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Found at i:1951 original size:22 final size:22
Alignment explanation
Indices: 1865--2134 Score: 72
Period size: 22 Copynumber: 12.1 Consensus size: 22
1855 AATTTTGAAG
* *
1865 ACCTCAATATGAAATTTTGATA
1 ACCTCCATATGAAATATTGATA
* * *
1887 ACTTCCCA-ATGAAATTTTGAGA
1 ACCT-CCATATGAAATATTGATA
** * * *
1909 ACCAACACCATGAGATGTTGATA
1 ACCTCCA-TATGAAATATTGATA
*
1932 ACCTCCATATGATATATTGATA
1 ACCTCCATATGAAATATTGATA
* ** * *
1954 ACCACGTTATGAAAATTTTGAAA
1 ACCTCCATATG-AAATATTGATA
* *
1977 ACCTCCATATGAATTGTT-AGTA
1 ACCTCCATATGAAATATTGA-TA
* *
1999 A--TCACACTCTGAAATTTTGATA
1 ACCTC-CA-TATGAAATATTGATA
2021 A--TCACACTATGAAAT-TGTGATA
1 ACCTC-CA-TATGAAATAT-TGATA
*
2043 ACCTCGC-TATGAAATTTTGATAA
1 ACCTC-CATATGAAATATTGAT-A
* * *
2066 ATCTTCC-TATAAAATTTTGATAA
1 A-CCTCCATATGAAATATTGAT-A
* * *
2089 ACCTCCCTATAAAATTTTGATA
1 ACCTCCATATGAAATATTGATA
** * * *
2111 AATTTCTTATGAAATCTTGATA
1 ACCTCCATATGAAATATTGATA
2133 AC
1 AC
2135 TACAAATTTT
Statistics
Matches: 192, Mismatches: 41, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.01
21 6 0.03
22 109 0.57
23 69 0.36
24 6 0.03
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
ACCTCCATATGAAATATTGATA
Found at i:2080 original size:23 final size:23
Alignment explanation
Indices: 2049--2133 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
2039 GATAACCTCG
*
2049 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
2072 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
2095 CTATAAAATTTTGATAAAT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
2117 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
2134 CTACAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 16 0.30
23 38 0.70
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:2132 original size:45 final size:45
Alignment explanation
Indices: 2010--2133 Score: 139
Period size: 45 Copynumber: 2.8 Consensus size: 45
2000 TCACACTCTG
* * *
2010 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
2054 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
*
2100 AAATTTTGATAAAT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
2134 CTACAAATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.45
46 27 0.39
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:2188 original size:22 final size:21
Alignment explanation
Indices: 2008--2280 Score: 126
Period size: 22 Copynumber: 12.6 Consensus size: 21
1998 AATCACACTC
**
2008 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAA-CTTACTA
* **
2030 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAA-CTTACTA
*
2052 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AA-CTTACTA
* **
2075 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AA-CTTACTA
* * *
2098 TAAAATTTTGATAAATTTCTTA
1 TGAAATTTTGATAACTTAC-TA
*
2120 TGAAATCTTGATAAC-TAC--
1 TGAAATTTTGATAACTTACTA
**
2138 --AAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAA-CTTACTA
** *
2158 TGATTTTTTGATAACTTAATTA
1 TGAAATTTTGATAACTT-ACTA
* **
2180 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAA-CTTACTA
* *
2202 TGAAATTTTGATCTACATACTA
1 TGAAATTTTGAT-AACTTACTA
* *
2224 TGAAATTTTGATAACCCT-CTTG
1 TGAAATTTTGATAA-CTTAC-TA
* *
2246 TGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAACT-TACTA
*
2268 TGAAAATTTGATA
1 TGAAATTTTGATA
2281 TCCTCCTTGA
Statistics
Matches: 190, Mismatches: 46, Indels: 30
0.71 0.17 0.11
Matches are distributed among these distances:
16 11 0.06
17 1 0.01
18 1 0.01
21 9 0.05
22 125 0.66
23 43 0.23
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACTTACTA
Found at i:2226 original size:44 final size:44
Alignment explanation
Indices: 1872--2295 Score: 207
Period size: 44 Copynumber: 9.7 Consensus size: 44
1862 AAGACCTCAA
* * *
1872 TATGAAATTTTGATAACTTCCCAATGAAATTTTGAGAACCA-ACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATA-AC
* * * * * * *
1917 CATGAGATGTTGATAACCTCCATATGATATATTGATAAC--CAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
* * *
1959 GTTATGAAAATTTTGAAAACCTCCATATG-AATTGTT-AGTAATCA-CAC
1 --TATG-AAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CATAAC
* * * * * * **
2006 TCTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
* * * * **
2050 TATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACATAAC
* ** * * *
2096 TATAAAATTTTGATAAATTTCTTATGAAATCTTGATAAC-T-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
** * *
2138 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACTTAAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
* * *
2178 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATAAC
* * *
2222 TATGAAATTTTGATAACC-CTCTTGTGAAATTTTGAAAAC-TAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACAT-AAC
* *
2266 TATGAAAATTTGATATCCT-CCT-TGAAATTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTT
2296 CGATTACTCC
Statistics
Matches: 293, Mismatches: 63, Indels: 49
0.72 0.16 0.12
Matches are distributed among these distances:
38 28 0.10
39 1 0.00
40 1 0.00
42 12 0.04
43 7 0.02
44 122 0.42
45 98 0.33
46 21 0.07
47 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
Found at i:2429 original size:22 final size:22
Alignment explanation
Indices: 2404--2454 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2394 TAATAACATT
2404 TGAAAATTGGATAACCTCTTTA
1 TGAAAATTGGATAACCTCTTTA
* *
2426 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTGGATAACCTCTTTA
2448 T-AAAATT
1 TGAAAATT
2455 TTGTTGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTGGATAACCTCTTTA
Found at i:2455 original size:22 final size:22
Alignment explanation
Indices: 2413--2457 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2403 TTGAAAATTG
*
2413 GATAACCTCTTTATGAAATTTT
1 GATAACCTCTTTATAAAATTTT
2435 GATAACCTCTTTATAAAATTTT
1 GATAACCTCTTTATAAAATTTT
2457 G
1 G
2458 TTGACCCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (22 bp):
GATAACCTCTTTATAAAATTTT
Found at i:2475 original size:22 final size:22
Alignment explanation
Indices: 2404--2567 Score: 66
Period size: 22 Copynumber: 7.3 Consensus size: 22
2394 TAATAACATT
* * * *
2404 TGAAAATTGGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
2426 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
2448 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* *
2470 TGAAATAAATTTTGATAATCCGATCTTTA
1 TG----AAATTTTGATAA-CC--CCTCTA
* * *
2499 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCCCTCTA
* *
2521 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAACCCCTCTA
* * *
2541 TCAAATTTTGGT-ACTCCT-TA
1 TGAAATTTTGATAACCCCTCTA
2561 TGAAATT
1 TGAAATT
2568 GAGACTTTTT
Statistics
Matches: 107, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
20 17 0.16
21 14 0.13
22 46 0.43
24 1 0.01
25 11 0.10
26 10 0.09
27 2 0.02
29 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:2617 original size:22 final size:22
Alignment explanation
Indices: 2588--2714 Score: 98
Period size: 22 Copynumber: 5.7 Consensus size: 22
2578 ATAACATTCA
*
2588 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCAC
* * *
2610 TATAAAATTTTTGATAATCTCCC
1 TATGAAA-TTTTGATAACCTCAC
* *
2633 TATGAAA-TATCAGTAACCTC-C
1 TATGAAATTTTGA-TAACCTCAC
* *
2654 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCTCAC
* *
2677 TATAAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCAC
*
2699 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
2715 TCTCTTTGAT
Statistics
Matches: 80, Mismatches: 18, Indels: 14
0.71 0.16 0.12
Matches are distributed among these distances:
21 7 0.09
22 49 0.61
23 24 0.30
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:2814 original size:24 final size:22
Alignment explanation
Indices: 2750--2837 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
2740 TTGTGATAAT
* *
2750 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
2772 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
2794 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
2818 TAACC-ACGCTATGAAATTTT
1 TAACCAAC-CTATGAAATTTT
2838 GAACAAAGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.02
22 35 0.66
24 17 0.32
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:3305 original size:31 final size:31
Alignment explanation
Indices: 3270--3335 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
3260 TGGAAATTTA
* * *
3270 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATATTTTAAA-AATAAGGATACAATCG
3301 GAAATATATTTTAAAAATAAGGATACAATCG
1 GAAATATATTTTAAAAATAAGGATACAATCG
3332 GAAA
1 GAAA
3336 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGATACAATCG
Found at i:7910 original size:91 final size:93
Alignment explanation
Indices: 7703--7930 Score: 325
Period size: 91 Copynumber: 2.5 Consensus size: 93
7693 TTCAGAAGAT
* * * *
7703 TTATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGATTCAATTATTGGAGAA
1 TTATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATAGCAGAA
* * *
7768 TTATACTGAATACCTAGTTATTGGGGAA
66 TTATACTGAAAACCCAGTTATTGGGAAA
* * * * *
7796 TTATTGAAAGAAAATCCATGTATGTAGAGTATTCTTCTTTCAAAGAAGATCCAATTATAGCATAA
1 TTATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATAGCAGAA
7861 -T-TACTGAAAACCCAGTTATTGGGAAA
66 TTATACTGAAAACCCAGTTATTGGGAAA
*
7887 TTATTGAAAGAAGATCCACGTATGTGGAGGATTCTTCTTTCAAA
1 TTATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
7931 TTATCAAAGA
Statistics
Matches: 119, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
91 62 0.52
92 1 0.01
93 56 0.47
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (93 bp):
TTATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATAGCAGAA
TTATACTGAAAACCCAGTTATTGGGAAA
Found at i:8100 original size:44 final size:44
Alignment explanation
Indices: 8017--8100 Score: 98
Period size: 45 Copynumber: 1.9 Consensus size: 44
8007 TGTTTGTTCA
** * * *
8017 AGATCAAGTTGTCAAGACCCTTGAATCAAATTATCATCAATTCG
1 AGATCAAGTCATCAAGACCCTCGAATCAAATCATAATCAATTCG
*
8061 AGATCAAGTCATCAAAGACCCTCGAATCGAATCA-AATCAA
1 AGATCAAGTCATC-AAGACCCTCGAATCAAATCATAATCAA
8101 ATTCCCAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
44 16 0.48
45 17 0.52
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (44 bp):
AGATCAAGTCATCAAGACCCTCGAATCAAATCATAATCAATTCG
Found at i:10379 original size:91 final size:91
Alignment explanation
Indices: 10224--10447 Score: 310
Period size: 91 Copynumber: 2.5 Consensus size: 91
10214 GCTTAAGAAG
* * *
10224 ATTGAAAGAAGATCCACGTATGTGGAAAATTTTTCTTTCAAAGAAGACTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT
* * *
10289 ACTGAAGA-CCTAGTTATTTGGG-AGTT
66 ACTGAAAATAC-AGTTA-TTGGGAAATT
* * *
10315 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTTAAAGAAGA-TCCAATTATTGCAGAAT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACT-CAATTATTGCAGAAT
10379 TACTGAAAATACAGTTATTGGGAAATT
65 TACTGAAAATACAGTTATTGGGAAATT
*
10406 ATTGAAAGAAGATCCACGTATGTGGAGGATTCTTCTTTCAAA
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
10448 TTATCAAAGA
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
90 6 0.05
91 111 0.94
92 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (91 bp):
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT
ACTGAAAATACAGTTATTGGGAAATT
Found at i:10717 original size:104 final size:100
Alignment explanation
Indices: 10532--10723 Score: 226
Period size: 104 Copynumber: 1.8 Consensus size: 100
10522 AATTTGTTTG
* *
10532 TTCAAGATCAAGTCGTCAAGACCCTTGAGTCAAATTATCATTAATTCGAGATCAAGTCATCAAAG
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATCAAATTATC--TAATTCAAGATCAAGTCATC--AG
* **
10597 ACCATCGAATCGAATCAAATCAAATTCCCAAGTCTTTAA
62 ACCATCAAATAAAATCAAATCAAATTCCCAAGTCTTTAA
*
10636 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATC-AATTCAAGATCAAGTCATTC-GACC
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATCAAATTATCTAATTCAAGATCAAGTCA-TCAGA-C
10699 CTTGAATCAAATAAAATCAAATCAA
64 C----ATCAAATAAAATCAAATCAA
10724 GTTCTCGACC
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
99 2 0.03
100 2 0.03
101 16 0.21
102 2 0.03
104 54 0.71
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.27
Consensus pattern (100 bp):
TTCAAGATCAAGTCGTCAAGACCCTTGAATCAAATTATCTAATTCAAGATCAAGTCATCAGACCA
TCAAATAAAATCAAATCAAATTCCCAAGTCTTTAA
Found at i:10734 original size:35 final size:35
Alignment explanation
Indices: 10693--10764 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
10683 ATCAAGTCAT
10693 TCGACCCTTGAATCAAATAAAATCAAATCAAGTTC
1 TCGACCCTTGAATCAAATAAAATCAAATCAAGTTC
10728 TCGACCCTTGAATCAAATAAAATCAAATCAAGTTC
1 TCGACCCTTGAATCAAATAAAATCAAATCAAGTTC
10763 TC
1 TC
10765 AAATTATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (35 bp):
TCGACCCTTGAATCAAATAAAATCAAATCAAGTTC
Found at i:11267 original size:70 final size:70
Alignment explanation
Indices: 11201--11417 Score: 353
Period size: 70 Copynumber: 3.1 Consensus size: 70
11191 GTTTTTATAG
* * * * *
11201 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
*
11266 TACTA
66 TACCA
11271 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
11336 TACCA
66 TACCA
* *
11341 TTTTACTCAAATAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
*
11406 TACAA
66 TACCA
11411 TTTTACT
1 TTTTACT
11418 ATTTTAGTTA
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 138 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (70 bp):
TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
TACCA
Found at i:12528 original size:23 final size:23
Alignment explanation
Indices: 12502--12545 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12492 TCGTTGGCGG
*
12502 ACTTGTACTGTTGGTTGTATCAT
1 ACTTGTACTGTTGGTAGTATCAT
12525 ACTTGTACTGTTGGTAGTATC
1 ACTTGTACTGTTGGTAGTATC
12546 TCAATTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (23 bp):
ACTTGTACTGTTGGTAGTATCAT
Found at i:23754 original size:19 final size:19
Alignment explanation
Indices: 23717--23755 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23707 CTTTTCTTCA
*
23717 AATAATTATTAAATAAATT
1 AATAATTAATAAATAAATT
* *
23736 AATAATTAATCAATCAATT
1 AATAATTAATAAATAAATT
23755 A
1 A
23756 GAGATAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATTAATAAATAAATT
Found at i:24415 original size:183 final size:182
Alignment explanation
Indices: 24053--24457 Score: 482
Period size: 183 Copynumber: 2.2 Consensus size: 182
24043 TTCTACCAAA
* * * *
24053 AAAATCTTCTAAAATAAAGTAGGTAGGATAGGATTGCATAATGCATATTATATGTTAATTTTCAT
1 AAAATCTTCTAAAATAAAGTAGGTACG-TAGGATTGCATTATACATATTATATGTTAATTTGCAT
* * *
24118 TATTGCCGAATTGATTAAAATATGTATGTGCATTTCACATGTAACTTTTTTTTTTTCAATTTTCT
65 TATTGCCGAATTGATTAAAATATGTATGAGCATGTCACATGTAACTTTTTTTTTTTCAATTCTCT
* * * *
24183 AACAAGGAAAAAGAAAATATTATTAGGGATTGTGACTTATAATTTTTTTTTAT
130 AACAAGCAAAAAAAAAATATTATCAGGCATTGTGACTTATAATTTTTTTTTAT
* ** * *
24236 AAAATCTACTAAAATATGGTAGGTATGTAGGATTGCATTATATATATTATAAT-TATAATTTGCA
1 AAAATCTTCTAAAATAAAGTAGGTACGTAGGATTGCATTATACATATTAT-ATGT-TAATTTGCA
*
24300 TTATTGCC-AAGTTGATTATAATATGTATGAGCATGTCACAT-TAAACTTTTTTTTTCTTTCCAA
64 TTATTGCCGAA-TTGATTAAAATATGTATGAGCATGTCACATGT-AAC-TTTTTTTT-TTT-CAA
*
24363 TTCTCTAACAAGACAAAAAAAAAATCTTATCAGGCA-TGTGAC-T-TAA-TTTTTTTTAT
124 TTCTCTAACAAG-CAAAAAAAAAATATTATCAGGCATTGTGACTTATAATTTTTTTTTAT
* * * *
24419 CAAGTCTTCTAAAATAAATTAAGTACGTAGGATTGCATT
1 AAAATCTTCTAAAATAAAGTAGGTACGTAGGATTGCATT
24458 TGCATTATAG
Statistics
Matches: 189, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
182 24 0.13
183 112 0.59
184 11 0.06
185 4 0.02
186 20 0.11
187 18 0.10
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (182 bp):
AAAATCTTCTAAAATAAAGTAGGTACGTAGGATTGCATTATACATATTATATGTTAATTTGCATT
ATTGCCGAATTGATTAAAATATGTATGAGCATGTCACATGTAACTTTTTTTTTTTCAATTCTCTA
ACAAGCAAAAAAAAAATATTATCAGGCATTGTGACTTATAATTTTTTTTTAT
Found at i:26447 original size:2 final size:2
Alignment explanation
Indices: 26442--26475 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26432 TCTCTTTTAA
26442 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
26476 TTGAGATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26947 original size:18 final size:19
Alignment explanation
Indices: 26921--26959 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
26911 GTTGTTCAAA
* *
26921 AACCGACCGTACCG-CCTG
1 AACCAACCGCACCGACCTG
26939 AACCAACCGCACCGACCTG
1 AACCAACCGCACCGACCTG
26958 AA
1 AA
26960 AATGTTGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.31, C:0.44, G:0.18, T:0.08
Consensus pattern (19 bp):
AACCAACCGCACCGACCTG
Found at i:35980 original size:21 final size:22
Alignment explanation
Indices: 35955--35996 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35945 CATTTTTCAG
35955 ATTTTAC-AAATTACAAATTTT
1 ATTTTACAAAATTACAAATTTT
* *
35976 ATTTTCCAAAATTACTAATTT
1 ATTTTACAAAATTACAAATTT
35997 CTTAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTACAAAATTACAAATTTT
Done.