Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008366.1 Corchorus capsularis cultivar CVL-1 contig08387, 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: 57808
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5354 original size:14 final size:15
Alignment explanation
Indices: 5327--5358 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5317 AGTCAAGATG
5327 AAGCTAAGAAAAAAA
1 AAGCTAAGAAAAAAA
5342 AAGCTAA-AAAAAAA
1 AAGCTAAGAAAAAAA
5356 AAG
1 AAG
5359 GAAAAAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.06
Consensus pattern (15 bp):
AAGCTAAGAAAAAAA
Found at i:11842 original size:22 final size:22
Alignment explanation
Indices: 11817--11988 Score: 109
Period size: 22 Copynumber: 7.8 Consensus size: 22
11807 ATGACCTCCT
*
11817 TATGAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAACCTTCC
* * * *
11839 TATGAAATTTTAAGAACCATAC
1 TATGAAATTTTGATAACCTTCC
* * **
11861 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
11883 TAT-TAATTTTTTTAAACCTTCT
1 TATGAAATTTTGAT-AACCTTCC
*
11905 TATGAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTTCC
11927 TAATG-AATTTTGA-AGACC-TCAC
1 T-ATGAAATTTTGATA-ACCTTC-C
* * * *
11949 TATCAAACTTTGCTAACTTTCC
1 TATGAAATTTTGATAACCTTCC
*
11971 AATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
11989 AACACTATGA
Statistics
Matches: 114, Mismatches: 28, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
21 11 0.10
22 89 0.78
23 14 0.12
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:13102 original size:44 final size:43
Alignment explanation
Indices: 13054--13933 Score: 198
Period size: 44 Copynumber: 20.1 Consensus size: 43
13044 AATCACACTC
*
13054 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* * * *
13098 TGAAATTTTGATAAAC-CTTCCTATAAAATTTTGATAATCTCCTTA
1 TGAAATTTTGATAATCAC--ACTATGAAATTTTGATAACCTCC-TA
* *
13143 TGAAATCTTG---AT-A-ACTA-CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCT-CCTA
** * * * * *
13181 TGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCT-CCTA
* * * * *
13225 TGAAATTTTGAT-CTACATATTATGAAACTTTGATAACCCTCTTA
1 TGAAATTTTGATAAT-CACACTATGAAATTTTGATAA-CCTCCTA
* * * *
13269 TGAAAATTTGA-AAACTAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAACC-TCCTA
* ** *
13313 TGAAATTTTGAT-ATC-CTCCCTGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCC-T-A
** * * ** * *
13355 T-AAAAGTT--TAATAAC-CTTTCTAA-TTTGGTAACCATACTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACC-TCCTA
* ** * * *
13394 TGAAATTTTGAT-ATC-CTCCCTGAAACTTTGGTAACCCTCTTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAA-CCTCCTA
* * * *
13436 TGAAAATTTGA-AAACTAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAACC-TCCTA
* * * * *
13480 TGACATTTTGAT-ATCTTC-C-ATGAAATTTTGATTACTTCATAA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAACCTCCT-A
** * ** * *
13522 T-AAAAGTT--TAATAAC-CT-TCCTAA-TTTGGTAACCATACTA
1 TGAAATTTTGATAATCACACTAT-GAAATTTTGATAACC-TCCTA
* * * * *
13561 TGAAATTTTGATAACCTTCCAAGAATACCACTATGAAATTTTGGTAATCGCATTT
1 TGAAATTTTGATAA---T-C------A-CACTATGAAATTTTGATAACCTC-CTA
* * ** *
13616 TAAAAATTTGATAAT-ATCTTTATGAAATTTTGTTAACCTCTCTA
1 TGAAATTTTGATAATCA-CACTATGAAATTTTGATAACCTC-CTA
* * * * * * *
13660 TAAAATTTTGTTGACCCCTCTATGAAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* * *
13704 TGAAATTTTGATAA-CAATACTATGAAATTTTGATAATCTTCCCA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAA-CCTCCTA
*
13748 T-AAATTTTGATAATCCGATCACTATGAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAAT-C-A-CACTATGAAATTTTGATAA-C-CTCCTA
* ** * *
13794 TGAGA-TTTGATAATC-TTCTATCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCC-TA
* * * * *
13834 TGAAATTGAGACTTTTATAACCTTCA-TATGAAATTTTGATAACCACATTA
1 TGAAA-T-----TTTGATAATC-ACACTATGAAATTTTGATAACCTC-CTA
** * *
13884 AAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCT-CCTA
13928 TGAAAT
1 TGAAAT
13934 ATTAGAAACC
Statistics
Matches: 596, Mismatches: 159, Indels: 162
0.65 0.17 0.18
Matches are distributed among these distances:
38 25 0.04
39 28 0.05
40 33 0.06
41 26 0.04
42 73 0.12
43 27 0.05
44 252 0.42
45 39 0.07
46 31 0.05
47 11 0.02
48 12 0.02
49 2 0.00
50 7 0.01
52 2 0.00
53 1 0.00
54 4 0.01
55 23 0.04
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (43 bp):
TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCTA
Found at i:13236 original size:82 final size:83
Alignment explanation
Indices: 13078--13236 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 83
13068 TCACACTATG
* *
13078 AAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAATCTCCTTA
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAATCTCCCTA
13143 TGAAATCTTGATAACTAC
66 TGAAATCTTGATAACTAC
* ** * * *
13161 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACC-TCATTATGAAATTTTGTTAATCTCCCT
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAAACCTTC-CTATAAAATTTTGATAATCTCCCT
*
13224 ATGAAATTTTGAT
65 ATGAAATCTTGAT
13237 CTACATATTA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
81 2 0.03
82 36 0.55
83 28 0.42
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (83 bp):
AAATTGTGATAACCTCCCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAATCTCCCTA
TGAAATCTTGATAACTAC
Found at i:13399 original size:81 final size:81
Alignment explanation
Indices: 13311--13573 Score: 289
Period size: 81 Copynumber: 3.2 Consensus size: 81
13301 ATAACCTTCA
13311 TATGAAATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTTCT
1 TATGAAATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTTCT
13376 AATTTGGTAACCATAC
66 AATTTGGTAACCATAC
* * * * * *
13392 TATGAAATTTTGATATCCTCCCTGAAACTTTGGTAAC-CCTCTTATGAAAA-TTTGAAAACTAAA
1 TATGAAATTTTGATATCCTCCCTGAAATTTTGATTACTCC-ATAAT-AAAAGTTT---AA-TAAC
* ** * *
13455 CTATGAAATTTTGATAACC-TTC
60 CTTTCTAA-TTTGGTAACCATAC
* * * * *
13477 ATATGACATTTTGATATCTTCCATGAAATTTTGATTACTTCATAATAAAAGTTTAATAACCTTCC
1 -TATGAAATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTTC
13542 TAATTTGGTAACCATAC
65 TAATTTGGTAACCATAC
13559 TATGAAATTTTGATA
1 TATGAAATTTTGATA
13574 ACCTTCCAAG
Statistics
Matches: 143, Mismatches: 28, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
80 2 0.01
81 63 0.44
82 13 0.09
83 2 0.01
84 2 0.01
85 14 0.10
86 46 0.32
87 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (81 bp):
TATGAAATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTTCT
AATTTGGTAACCATAC
Found at i:13434 original size:167 final size:167
Alignment explanation
Indices: 13247--13573 Score: 600
Period size: 167 Copynumber: 2.0 Consensus size: 167
13237 CTACATATTA
13247 TGAAACTTTGATAACCCTCTTATGAAAATTTGAAAACTAAACTATGAAATTTTGATAACCTTCAT
1 TGAAACTTTGATAACCCTCTTATGAAAATTTGAAAACTAAACTATGAAATTTTGATAACCTTCAT
* *
13312 ATGAAATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTTCTA
66 ATGAAATTTTGATATCCTCCATGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTA
13377 ATTTGGTAACCATACTATGAAATTTTGATATCCTCCC
131 ATTTGGTAACCATACTATGAAATTTTGATATCCTCCC
*
13414 TGAAACTTTGGTAACCCTCTTATGAAAATTTGAAAACTAAACTATGAAATTTTGATAACCTTCAT
1 TGAAACTTTGATAACCCTCTTATGAAAATTTGAAAACTAAACTATGAAATTTTGATAACCTTCAT
* * *
13479 ATGACATTTTGATATCTTCCATGAAATTTTGATTACTTCATAATAAAAGTTTAATAACCTTCCTA
66 ATGAAATTTTGATATCCTCCATGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTA
13544 ATTTGGTAACCATACTATGAAATTTTGATA
131 ATTTGGTAACCATACTATGAAATTTTGATA
13574 ACCTTCCAAG
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 154 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (167 bp):
TGAAACTTTGATAACCCTCTTATGAAAATTTGAAAACTAAACTATGAAATTTTGATAACCTTCAT
ATGAAATTTTGATATCCTCCATGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTA
ATTTGGTAACCATACTATGAAATTTTGATATCCTCCC
Found at i:13438 original size:42 final size:42
Alignment explanation
Indices: 13247--13446 Score: 117
Period size: 42 Copynumber: 4.8 Consensus size: 42
13237 CTACATATTA
* **
13247 TGAAACTTTGATAACCCTCTTATGAAAATTTGA-AAACTAAACTA
1 TGAAACTTTGATAACCCTCTTATGAAAATTTGATAACCT---CCC
* * * * *
13291 TGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTCCC
1 TGAAACTTTGATAACCCTCTTATGAAAATTTGATAACCTCCC
* * * * * **
13333 TGAAATTTTGATTACTCC-ATAAT-AAAAGTTTAATAACCTTTC
1 TGAAACTTTGATAAC-CCTCTTATGAAAA-TTTGATAACCTCCC
* * * *
13375 T--AA-TTTGGTAACCATAC-TATGAAATTTTGATATCCTCCC
1 TGAAACTTTGATAACCCT-CTTATGAAAATTTGATAACCTCCC
*
13414 TGAAACTTTGGTAACCCTCTTATGAAAATTTGA
1 TGAAACTTTGATAACCCTCTTATGAAAATTTGA
13447 AAACTAAACT
Statistics
Matches: 116, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
38 1 0.01
39 20 0.17
40 5 0.04
41 6 0.05
42 51 0.44
43 1 0.01
44 29 0.25
45 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (42 bp):
TGAAACTTTGATAACCCTCTTATGAAAATTTGATAACCTCCC
Found at i:13481 original size:22 final size:22
Alignment explanation
Indices: 13054--13579 Score: 173
Period size: 22 Copynumber: 24.9 Consensus size: 22
13044 AATCACACTC
* *
13054 TGAAATTTTGATAATC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
13076 TGAAATTGTGATAACC-TCGCTA
1 TGAAATTTTGATAACCTTC-ATA
*
13098 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTTCATA
* * * *
13121 TAAAATTTTGATAATCTCCTTA
1 TGAAATTTTGATAACCTTCATA
*
13143 TGAAATCTTGATAA----C-TA
1 TGAAATTTTGATAACCTTCATA
* * *
13160 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTTCATA
**
13181 TGATTTTTTGATAACC-TCATTA
1 TGAAATTTTGATAACCTTCA-TA
* * * *
13203 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTTCATA
* *
13225 TGAAATTTTGATCTA-CAT-ATTA
1 TGAAATTTTGAT-AACCTTCA-TA
* * *
13247 TGAAACTTTGATAACCCTCTTA
1 TGAAATTTTGATAACCTTCATA
* * **
13269 TGAAAATTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCTTCA-TA
13291 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCATA
* **
13313 TGAAATTTTGATATCC-TC-CC
1 TGAAATTTTGATAACCTTCATA
* *
13333 TGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAACCTTCAT-A
* * * *
13355 TAAAAGTTTAATAACCTT--TC
1 TGAAATTTTGATAACCTTCATA
* *
13375 T--AA-TTTGGTAACCAT-ACTA
1 TGAAATTTTGATAACCTTCA-TA
* **
13394 TGAAATTTTGATATCC-TC-CC
1 TGAAATTTTGATAACCTTCATA
* * * *
13414 TGAAACTTTGGTAACCCTCTTA
1 TGAAATTTTGATAACCTTCATA
* * **
13436 TGAAAATTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCTTCA-TA
13458 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCATA
* * *
13480 TGACATTTTGAT-ATCTTC-CA
1 TGAAATTTTGATAACCTTCATA
*
13500 TGAAATTTTGATTA-CTTCATAA
1 TGAAATTTTGATAACCTTCAT-A
* * * *
13522 TAAAAGTTTAATAACCTTC--C
1 TGAAATTTTGATAACCTTCATA
* *
13542 T--AA-TTTGGTAACCAT-ACTA
1 TGAAATTTTGATAACCTTCA-TA
13561 TGAAATTTTGATAACCTTC
1 TGAAATTTTGATAACCTTC
13580 CAAGAATACC
Statistics
Matches: 365, Mismatches: 97, Indels: 83
0.67 0.18 0.15
Matches are distributed among these distances:
16 11 0.03
17 20 0.05
18 5 0.01
19 4 0.01
20 45 0.12
21 26 0.07
22 216 0.59
23 36 0.10
24 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:13647 original size:22 final size:22
Alignment explanation
Indices: 13622--14009 Score: 176
Period size: 22 Copynumber: 17.6 Consensus size: 22
13612 ATTTTAAAAA
** *
13622 TTTGATAATATCTTTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
13644 TTTGTTAACCTCTCTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
13666 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
13688 TTTGATAACCTCGCTTTGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
13710 TTTGATAACAAT-ACTATGAAAT
1 TTTGATAAC-CTCTCTATGAAAT
* *
13732 TTTGATAATCT-TCCCAT-AAAT
1 TTTGATAACCTCT-CTATGAAAT
*
13753 TTTGATAATCCGATCACTATGAAAT
1 TTTGATAA-CC--TCTCTATGAAAT
* * * *
13778 TTCGATAATCACTCTATGAGA-
1 TTTGATAACCTCTCTATGAAAT
* *
13799 TTTGATAATCT-TCTATCAAAT
1 TTTGATAACCTCTCTATGAAAT
*
13820 TTTGGT-A-CTC-CTTATGAAATT
1 TTTGATAACCTCTC-TATGAAA-T
*
13841 GAGACTTTTATAACCT-TCATATGAAAT
1 -----TTTGATAACCTCTC-TATGAAAT
* **
13868 TTTGATAACCACAT-TAAAAAAT
1 TTTGATAACCTC-TCTATGAAAT
* *
13890 TTTGATAACCACACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
13912 TTTGATAACCTCCCCATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
13934 ATTAGA-AA-C-CTC-ATAAAAT
1 -TTTGATAACCTCTCTATGAAAT
* * * *
13953 TTTGTTAACCACACTATTAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
13975 TCTT-ATAACCTCGCTATGACAT
1 T-TTGATAACCTCTCTATGAAAT
*
13997 TTTGATAATCTCT
1 TTTGATAACCTCT
14010 TTGATAACCT
Statistics
Matches: 276, Mismatches: 61, Indels: 58
0.70 0.15 0.15
Matches are distributed among these distances:
18 3 0.01
19 11 0.04
20 17 0.06
21 33 0.12
22 172 0.62
23 7 0.03
24 6 0.02
25 11 0.04
26 4 0.01
27 2 0.01
28 10 0.04
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTGATAACCTCTCTATGAAAT
Found at i:13790 original size:20 final size:20
Alignment explanation
Indices: 13723--13808 Score: 57
Period size: 21 Copynumber: 3.9 Consensus size: 20
13713 GATAACAATA
*
13723 CTATGAAATTTTGATAATCTTC
1 CTATGAAA-TTTGATAATC-AC
*
13745 CCAT-AAATTTTGATAATCCGATC
1 CTATGAAA-TTTGATAAT-C-A-C
13768 ACTATGAAATTTCGATAATCAC
1 -CTATGAAATTT-GATAATCAC
*
13790 TCTATGAGATTTGATAATC
1 -CTATGAAATTTGATAATC
13809 TTCTATCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
21 20 0.38
22 15 0.28
23 2 0.04
24 7 0.13
25 9 0.17
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (20 bp):
CTATGAAATTTGATAATCAC
Found at i:14121 original size:22 final size:22
Alignment explanation
Indices: 14093--14243 Score: 105
Period size: 22 Copynumber: 6.8 Consensus size: 22
14083 ACATGATCCT
*
14093 ATGAAATTTTGGTAACCACACC
1 ATGAAATTTTGATAACCACACC
*
14115 ATGAAATTTTGATAACCTTC-CC
1 ATGAAATTTTGATAACC-ACACC
*
14137 ATGAAATTTTGATAACTTC-CA-T
1 ATGAAATTTTGATAAC--CACACC
* *
14159 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCACACC
* *
14181 ATGGAATTTTGAATAACCTC-CTC
1 ATGAAATTTTG-ATAACCACAC-C
* * * **
14204 ATGAAATTATAATAATCATC-TT
1 ATGAAATTTTGATAACCA-CACC
14226 ATGAAATTTTGATAACCA
1 ATGAAATTTTGATAACCA
14244 TACAGAGACA
Statistics
Matches: 102, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 82 0.80
23 16 0.16
24 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:14163 original size:44 final size:43
Alignment explanation
Indices: 14089--14242 Score: 141
Period size: 44 Copynumber: 3.5 Consensus size: 43
14079 AATAACATGA
* *
14089 TCCTATGAAATTTTGGTAACCACAC-CATGAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACCTC-CTCATGAAATTTTGATAACC
* * *
14132 TTCCCATGAAATTTTGATAACTTCCAT-ATGAAATTTTGGTAACC
1 -TCCTATGAAATTTTGATAACCTCC-TCATGAAATTTTGATAACC
* * * * *
14176 ACACTATGGAATTTTGAATAACCTCCTCATGAAATTATAATAATCA
1 TC-CTATGAAATTTTG-ATAACCTCCTCATGAAATTTTGATAA-CC
*
14222 TCTTATGAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACC
14243 ATACAGAGAC
Statistics
Matches: 88, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
43 2 0.02
44 53 0.60
45 31 0.35
46 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (43 bp):
TCCTATGAAATTTTGATAACCTCCTCATGAAATTTTGATAACC
Found at i:14208 original size:67 final size:66
Alignment explanation
Indices: 14092--14243 Score: 200
Period size: 67 Copynumber: 2.3 Consensus size: 66
14082 AACATGATCC
* * *
14092 TATGAAATTTTGGTAACCACACCATGAAATTTTGATAACCTTCCCATGAAATTTTGATAA-CTTC
1 TATGAAATTTTGGTAACCACACCATGAAATTTTGATAACCTTCCCATGAAATTATAATAATCAT-
14156 CA
65 CA
* *
14158 TATGAAATTTTGGTAACCACACTATGGAATTTTGAATAACC-TCCTCATGAAATTATAATAATCA
1 TATGAAATTTTGGTAACCACACCATGAAATTTTG-ATAACCTTCC-CATGAAATTATAATAATCA
*
14222 TCT
64 TCA
*
14225 TATGAAATTTTGATAACCA
1 TATGAAATTTTGGTAACCA
14244 TACAGAGACA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
66 35 0.46
67 39 0.51
68 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (66 bp):
TATGAAATTTTGGTAACCACACCATGAAATTTTGATAACCTTCCCATGAAATTATAATAATCATC
A
Found at i:16692 original size:24 final size:24
Alignment explanation
Indices: 16647--16693 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16637 ATTTTGATAG
* *
16647 TGGATAGTTAAACGTTTTCGGTTT
1 TGGATAGTGAAACATTTTCGGTTT
16671 TGGATAGTGAAA-ATTTTACGGTT
1 TGGATAGTGAAACATTTT-CGGTT
16694 ATCCACACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (24 bp):
TGGATAGTGAAACATTTTCGGTTT
Found at i:19624 original size:21 final size:21
Alignment explanation
Indices: 19595--19651 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19585 GCATAACTTG
* *
19595 GAATCGATTGGAATACTCCTA
1 GAATCGATTGGAATACACATA
* * *
19616 GAATTGATTGTAATAGACATA
1 GAATCGATTGGAATACACATA
19637 GAATCGATTGGAATA
1 GAATCGATTGGAATA
19652 TTCTTTCTCC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (21 bp):
GAATCGATTGGAATACACATA
Found at i:25911 original size:6 final size:6
Alignment explanation
Indices: 25897--25932 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
25887 AAGACTAAGC
*
25897 AAAT-T AAATTT AAATCT AAATCT AAATCT AAATCT A
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT A
25933 TGGCAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATCT
Found at i:30212 original size:15 final size:15
Alignment explanation
Indices: 30192--30232 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
30182 TCTAAGTTGT
*
30192 TCATCTTCTTGTGGC
1 TCATCTTCTGGTGGC
30207 TCATCTTCTGGTGGC
1 TCATCTTCTGGTGGC
30222 TCATCTTCTGG
1 TCATCTTCTGG
30233 CTTAGCAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.27, G:0.22, T:0.44
Consensus pattern (15 bp):
TCATCTTCTGGTGGC
Found at i:37454 original size:78 final size:78
Alignment explanation
Indices: 37365--37527 Score: 299
Period size: 78 Copynumber: 2.1 Consensus size: 78
37355 TTTTTTTAAC
* *
37365 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
37430 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
37443 TGAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
37508 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
37521 TAAAATA
1 TAAAATA
37528 AAATAATTAT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:37555 original size:62 final size:62
Alignment explanation
Indices: 37458--37587 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 62
37448 TAGTAAAATG
* * * *
37458 GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGA
1 GTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
*
37520 GTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
1 GTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
*
37582 CTAAAA
1 GTAAAA
37588 CTATAAAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (62 bp):
GTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
Found at i:49326 original size:12 final size:12
Alignment explanation
Indices: 49309--49339 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49299 AGAATTTCAC
49309 TCTCTTTCTTTT
1 TCTCTTTCTTTT
49321 TCTCTTTCTTTT
1 TCTCTTTCTTTT
49333 TCTCTTT
1 TCTCTTT
49340 TTCTTGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTCTTTCTTTT
Found at i:52250 original size:2 final size:2
Alignment explanation
Indices: 52243--52268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52233 ATGGAGATTA
52243 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
52269 TCATTAAAGT
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):
AT
Found at i:57275 original size:11 final size:11
Alignment explanation
Indices: 57259--57285 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
57249 ACCAACTGCA
57259 AAAAATAAAAT
1 AAAAATAAAAT
57270 AAAAATAAAAT
1 AAAAATAAAAT
57281 AAAAA
1 AAAAA
57286 AGAGGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:57538 original size:1 final size:1
Alignment explanation
Indices: 57502--57529 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
57492 AGGTGAAGGG
57502 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
57530 CCCTAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.