Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014704.1 Corchorus capsularis cultivar CVL-1 contig14725, 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: 25003
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:3050 original size:38 final size:38
Alignment explanation
Indices: 3004--3129 Score: 141
Period size: 38 Copynumber: 3.3 Consensus size: 38
2994 ACCATGATAA
3004 TTGGTCGCTTGGGTCTTGATCAAAAGCGAATAATAAGT
1 TTGGTCGCTTGGGTCTTGATCAAAAGCGAATAATAAGT
* * * * *
3042 TTGATCGCTT---TGTTGACACCAGGACAATCGAATAATAAAT
1 TTGGTCGCTTGGGTCTTG--ATCA--A-AAGCGAATAATAAGT
3082 TTGGTCGCTTGGGTCTTGATCAAAAGCGAATAATAAGT
1 TTGGTCGCTTGGGTCTTGATCAAAAGCGAATAATAAGT
3120 TTGGTCGCTT
1 TTGGTCGCTT
3130 TGTTGCAAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
35 4 0.06
37 3 0.04
38 32 0.46
39 2 0.03
40 22 0.31
41 3 0.04
43 4 0.06
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (38 bp):
TTGGTCGCTTGGGTCTTGATCAAAAGCGAATAATAAGT
Found at i:3173 original size:10 final size:10
Alignment explanation
Indices: 3158--3182 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3148 GAAGCCTACA
3158 AATTACAATT
1 AATTACAATT
3168 AATTACAATT
1 AATTACAATT
3178 AATTA
1 AATTA
3183 GTGTTAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTACAATT
Found at i:4837 original size:15 final size:16
Alignment explanation
Indices: 4808--4839 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4798 AATGCAGAAG
4808 GCAGAAAAGCTCTGAA
1 GCAGAAAAGCTCTGAA
4824 GCAGAAAA-CTCTGAA
1 GCAGAAAAGCTCTGAA
4839 G
1 G
4840 AATCAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (16 bp):
GCAGAAAAGCTCTGAA
Found at i:6801 original size:15 final size:16
Alignment explanation
Indices: 6781--6814 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
6771 TCAAAAAATT
6781 AAATATTTTTTTAA-A
1 AAATATTTTTTTAATA
6796 AAATATTTTTTTAATA
1 AAATATTTTTTTAATA
6812 AAA
1 AAA
6815 AAATGTGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATATTTTTTTAATA
Found at i:6867 original size:29 final size:29
Alignment explanation
Indices: 6835--6893 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
6825 TGGCAGATGA
*
6835 CACGTCAGCACAGTTGACGTCGTCACTGC
1 CACGTCAGCACAGTTGACATCGTCACTGC
6864 CACGTCAGCACAGTTGACATCGTCACTGC
1 CACGTCAGCACAGTTGACATCGTCACTGC
6893 C
1 C
6894 GGCTTGTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.20
Consensus pattern (29 bp):
CACGTCAGCACAGTTGACATCGTCACTGC
Found at i:7207 original size:13 final size:13
Alignment explanation
Indices: 7189--7213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7179 TATTGATGGT
7189 TAAAATCTAAAGA
1 TAAAATCTAAAGA
7202 TAAAATCTAAAG
1 TAAAATCTAAAG
7214 GGAATGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
TAAAATCTAAAGA
Found at i:8942 original size:29 final size:30
Alignment explanation
Indices: 8910--8967 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
8900 AGTTGTTAAA
* *
8910 TTTTGGATG-TTTTTGCATAAATTTTAAGG
1 TTTTGGATGCTCTTGGCATAAATTTTAAGG
*
8939 TTTTGGATGCTCTTGGCATAACTTTTAAG
1 TTTTGGATGCTCTTGGCATAAATTTTAAG
8968 TTCGGATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (30 bp):
TTTTGGATGCTCTTGGCATAAATTTTAAGG
Found at i:10904 original size:16 final size:16
Alignment explanation
Indices: 10883--10917 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10873 AGTATGGAAA
10883 AGACAAGAGAATATAG
1 AGACAAGAGAATATAG
* *
10899 AGACAATAGAATATGG
1 AGACAAGAGAATATAG
10915 AGA
1 AGA
10918 AGAAGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.26, T:0.14
Consensus pattern (16 bp):
AGACAAGAGAATATAG
Found at i:11148 original size:11 final size:11
Alignment explanation
Indices: 11134--11171 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11124 ATTCATAACA
11134 AATTTATAATT
1 AATTTATAATT
11145 AATTTATAATT
1 AATTTATAATT
11156 -ATTTGATAATT
1 AATTT-ATAATT
*
11167 TATTT
1 AATTT
11172 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:11422 original size:31 final size:31
Alignment explanation
Indices: 11376--11446 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
11366 GTGGAAATTT
*
11376 TATATTTTCCGATTATACCCTTATT-TTTAAAA
1 TATA-TTTCCAATTATACCCTT-TTATTTAAAA
11408 TATATTTCCAATTATACCCTTTTATTTAAAA
1 TATATTTCCAATTATACCCTTTTATTTAAAA
*
11439 CATATTTC
1 TATATTTC
11447 TAAATTACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 2 0.06
31 30 0.83
32 4 0.11
ACGTcount: A:0.32, C:0.17, G:0.01, T:0.49
Consensus pattern (31 bp):
TATATTTCCAATTATACCCTTTTATTTAAAA
Found at i:11750 original size:22 final size:22
Alignment explanation
Indices: 11722--11849 Score: 91
Period size: 22 Copynumber: 5.7 Consensus size: 22
11712 TGTCTCTATG
11722 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
11744 TGGTTATTATAATTCCATGATGA
1 TGGTTATCAAAATTTCAT-AAGA
*
11767 -GGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
11788 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* *
11810 TTAGGTTATTAAAATTTC-TTAGA
1 -T-GGTTATCAAAATTTCATAAGA
**
11833 TTGGTTATTGAAATTTC
1 -TGGTTATCAAAATTTC
11850 GTAAAGTGGT
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.01
22 59 0.71
23 10 0.12
24 13 0.16
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:11847 original size:46 final size:43
Alignment explanation
Indices: 11723--11849 Score: 114
Period size: 46 Copynumber: 2.8 Consensus size: 43
11713 GTCTCTATGT
* *
11723 GGTTATCAAAATTTCATAAGA-TGGTTATTATAATTCCATGATGA
1 GGTTATCAAAATTTC-TTAGATTGGTTATTA-AATTTCATGATGA
* ** *
11767 GGTTATCAAAATTTCATAG-TGTGGTTACCAAAATTTCATAGGATTA
1 GGTTATCAAAATTTCTTAGAT-TGGTTA-TTAAATTTCAT--GATGA
*
11813 GGTTATTAAAATTTCTTAGATTGGTTATTGAAATTTC
1 GGTTATCAAAATTTCTTAGATTGGTTATT-AAATTTC
11850 GTAAAGTGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
43 2 0.03
44 28 0.42
45 1 0.02
46 34 0.52
47 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.41
Consensus pattern (43 bp):
GGTTATCAAAATTTCTTAGATTGGTTATTAAATTTCATGATGA
Found at i:11859 original size:22 final size:22
Alignment explanation
Indices: 11813--11861 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11803 CATAGGATTA
* * *
11813 GGTTATTAAAATTTCTTAGATT
1 GGTTATTAAAATTTCGTAAAGT
*
11835 GGTTATTGAAATTTCGTAAAGT
1 GGTTATTAAAATTTCGTAAAGT
11857 GGTTA
1 GGTTA
11862 GTTATCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (22 bp):
GGTTATTAAAATTTCGTAAAGT
Found at i:11950 original size:22 final size:22
Alignment explanation
Indices: 11900--12030 Score: 81
Period size: 22 Copynumber: 6.0 Consensus size: 22
11890 AAAAAGATTT
* *
11900 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
11923 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
11944 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
11965 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
11988 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
12010 CAAAATTTCATA-TGAAGGTTA
1 CAAAATTTCATAGTG-AGGTTA
12031 TAAAGGTCTC
Statistics
Matches: 82, Mismatches: 20, Indels: 13
0.71 0.17 0.11
Matches are distributed among these distances:
21 8 0.10
22 69 0.84
23 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:12031 original size:22 final size:22
Alignment explanation
Indices: 11925--12287 Score: 128
Period size: 22 Copynumber: 16.3 Consensus size: 22
11915 AGGTTATACG
* *
11925 AATTTCATAGTG-TGGTTAACAA
1 AATTTCATA-TGAAGGTTATCAA
11947 AATTTCAT-TAGAAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* * ** *
11969 TACTTCATCGGGAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
11991 AATTTTATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
12013 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * * *
12034 AGGTCTCGATTTCAT-AAGGAGTACCAA
1 A-ATTTC-A--T-ATGAAGG-TTATCAA
*
12061 AATTTGATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
*
12081 AATCTCATA-G-AGTGATTATCAA
1 AATTTCATATGAAG-G-TTATCAA
* *
12103 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT-ATGA-A-GGTTATCAA
*
12128 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
* **
12149 ATTTTCATA-GTATTGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
*
12171 AATTTCA-AAGCAAGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
** * *
12193 AATTAAATAATG-TGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
* * *
12215 AATTTCATA-GAGGGGTCAACAA
1 AATTTCATATGA-AGGTTATCAA
* * *
12237 AATTTTATAAGAATGTTATCAA
1 AATTTCATATGAAGGTTATCAA
*
12259 AATTTCATA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
12281 ATTTTCA
1 AATTTCA
12288 AAATGTGATT
Statistics
Matches: 254, Mismatches: 55, Indels: 64
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.01
20 12 0.05
21 32 0.13
22 164 0.65
23 10 0.04
24 5 0.02
25 18 0.07
26 7 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:12278 original size:66 final size:65
Alignment explanation
Indices: 12042--12287 Score: 193
Period size: 66 Copynumber: 3.8 Consensus size: 65
12032 AAAGGTCTCG
* * * * *
12042 ATTTCATAAGGA-G-TACCAAAATTTGATAGA-AGGTTATC-AAATCTCATAGAGTGATTATCAA
1 ATTTCATAAGAATGTTATCAAAATTT-ATAAAGAGGTTATCAAAATTTCATAGAGTGGTTATCAA
12103 A
65 A
* *
12104 ATTTCATAAAGATATGATTATCAAAATTTATATGAAGA--TTATCAAATTTTCATAGTA-TTGTT
1 ATTTCAT-AAGA-ATG-TTATCAAAATTTATA--AAGAGGTTATCAAAATTTCATAG-AGTGGTT
12166 ATCAAA
60 ATCAAA
* * * * * * * *
12172 ATTTCA-AAGCAAGGTTATCAAAATTAAATAATGTGATTATCAAAATTTCATAGAGGGGTCAACA
1 ATTTCATAAG-AATGTTATCAAAATT-TATAAAGAGGTTATCAAAATTTCATAGAGTGGTTATCA
12236 AA
64 AA
* *
12238 ATTTTATAAGAATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 ATTTCATAAGAATGTTATCAAAATTT-ATAAAGAGGTTATCAAAATTTCA
12288 AAATGTGATT
Statistics
Matches: 144, Mismatches: 23, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
62 7 0.05
63 3 0.02
64 3 0.02
65 13 0.09
66 72 0.50
67 19 0.13
68 25 0.17
69 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (65 bp):
ATTTCATAAGAATGTTATCAAAATTTATAAAGAGGTTATCAAAATTTCATAGAGTGGTTATCAAA
Found at i:12429 original size:19 final size:19
Alignment explanation
Indices: 12399--12465 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
12389 TGATGGAGTA
12399 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
12419 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
*
12438 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
12457 ATCAAAATT
1 ATCAAAATT
12466 TCATATGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 38 0.86
20 6 0.14
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:12484 original size:22 final size:22
Alignment explanation
Indices: 12456--12721 Score: 87
Period size: 22 Copynumber: 12.5 Consensus size: 22
12446 TCAGTGAGGA
12456 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
12478 TATCAAATTTTCATGGTTTA-GT
1 TATCAAAATTTCAT-ATGAAGGT
* *
12500 TTTCAAAATTTCATAAG-AGG-
1 TATCAAAATTTCATATGAAGGT
* * * *
12520 ---GAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
**
12539 TAAAAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
12561 TATCAACAA-ATCATAGGGAGCT
1 TATCAA-AATTTCATATGAAGGT
*
12583 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
12599 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
12621 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * *
12644 TATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
12667 TATCAAAATTTCATA-GCAAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
12689 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
12711 TATCAAAATTT
1 TATCAAAATTT
12722 TAAAGTGTGA
Statistics
Matches: 182, Mismatches: 41, Indels: 42
0.69 0.15 0.16
Matches are distributed among these distances:
16 8 0.04
17 14 0.08
18 4 0.02
20 3 0.02
21 7 0.04
22 103 0.57
23 42 0.23
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:12651 original size:23 final size:23
Alignment explanation
Indices: 12598--12723 Score: 98
Period size: 22 Copynumber: 5.6 Consensus size: 23
12588 AAATTTGTAG
* * * *
12598 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
12620 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
12643 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
* * *
12666 TTATCAAAATTTCATAGCAAG-G
1 TTATCAAAATTTTATAGGAAGAT
* * *
12688 TTATCACAATTTCATAGTG-TGA-
1 TTATCAAAATTTTATAG-GAAGAT
12710 TTATCAAAATTTTA
1 TTATCAAAATTTTA
12724 AAGTGTGATT
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
22 45 0.54
23 38 0.46
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:12728 original size:22 final size:22
Alignment explanation
Indices: 12688--12734 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
12678 CATAGCAAGG
* *
12688 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
*
12710 TTATCAAAATTTTAAAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
12732 TTA
1 TTA
12735 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGTGTGA
Found at i:12802 original size:22 final size:22
Alignment explanation
Indices: 12774--12880 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 22
12764 TTTATAAAGT
*
12774 GGTTATCAATATATCATATGGA
1 GGTTATCAAAATATCATATGGA
* * **
12796 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATATCATA-TGGA
* *
12819 GGTTATCAAAATTTCATATTGA
1 GGTTATCAAAATATCATATGGA
* * *
12841 GCTCT-TCAAAAT-TCCTTAGGGA
1 GGT-TATCAAAATAT-CATATGGA
* *
12863 GGTTAACAAAATTTCATA
1 GGTTATCAAAATATCATA
12881 AGAAAGTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
21 2 0.03
22 42 0.66
23 20 0.31
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATATCATATGGA
Found at i:12826 original size:23 final size:22
Alignment explanation
Indices: 12772--12837 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
12762 TTTTTATAAA
*
12772 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* * *
12794 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
12817 TTGGTTATCAAAATTTCATAT
1 GTGGTTATCAAAATATCATAT
12838 TGAGCTCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:18007 original size:21 final size:21
Alignment explanation
Indices: 17983--18026 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17973 CAAGGCAGAG
* *
17983 CCGCCACCAGCACCGCCAACT
1 CCGCCACCACCACCACCAACT
*
18004 CCGCCACCACCATCACCAACT
1 CCGCCACCACCACCACCAACT
18025 CC
1 CC
18027 AAGCAAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.59, G:0.09, T:0.07
Consensus pattern (21 bp):
CCGCCACCACCACCACCAACT
Found at i:19914 original size:18 final size:19
Alignment explanation
Indices: 19884--19923 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
19874 TTATTAAAAT
*
19884 TTACTATATAATATTAATA
1 TTACTATATAATAATAATA
19903 TTACTA-ATAATAATAATA
1 TTACTATATAATAATAATA
19921 TTA
1 TTA
19924 TTTAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TTACTATATAATAATAATA
Found at i:21397 original size:19 final size:19
Alignment explanation
Indices: 21373--21412 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
21363 CTTTTCAGAT
*
21373 ATTTCTACAATTATATACC
1 ATTTCTAAAATTATATACC
21392 ATTTCTAAAATTATATACC
1 ATTTCTAAAATTATATACC
21411 AT
1 AT
21413 ATATTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTCTAAAATTATATACC
Found at i:21591 original size:20 final size:21
Alignment explanation
Indices: 21568--21610 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
21558 TAATCGGGTC
* *
21568 AAAACACGATTAACACG-TTT
1 AAAACACAAGTAACACGCTTT
21588 AAAACACAAGTAACACGCTTT
1 AAAACACAAGTAACACGCTTT
21609 AA
1 AA
21611 TTAACAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAACACAAGTAACACGCTTT
Found at i:24293 original size:42 final size:42
Alignment explanation
Indices: 24245--24365 Score: 215
Period size: 42 Copynumber: 2.9 Consensus size: 42
24235 AAAATAGCGT
**
24245 TAACGTGTTGTATTTTGATGACGATTTAAGAAAAATGAACCA
1 TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAACCA
24287 TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAACCA
1 TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAACCA
*
24329 TAACGTGCCGTATTTTGATGACGATTTCAGAAAAATG
1 TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
24366 CAATTTTTGA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (42 bp):
TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAACCA
Done.