Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013924.1 Corchorus olitorius cultivar O-4 contig13957, 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: 62169
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4107 original size:31 final size:31
Alignment explanation
Indices: 4064--4135 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
4054 GGTAATTTTC
* * *
4064 TCAGATCATTCGGGTTTCGGCTCATCTGGAT
1 TCAGGTCATTCGGATCTCGGCTCATCTGGAT
* *
4095 TCAGGTCATTCGGATCTCGGGTCTTCTGGAT
1 TCAGGTCATTCGGATCTCGGCTCATCTGGAT
*
4126 TTAGGGTCAT
1 TCA-GGTCAT
4136 GCAGGTTCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (31 bp):
TCAGGTCATTCGGATCTCGGCTCATCTGGAT
Found at i:4379 original size:21 final size:22
Alignment explanation
Indices: 4355--4395 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4345 GTTTATAATA
4355 TTCTTGGGTCA-TCGGGTTATC
1 TTCTTGGGTCATTCGGGTTATC
*
4376 TTCTTGGGTTATTCGGGTTA
1 TTCTTGGGTCATTCGGGTTA
4396 CGAGTTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (22 bp):
TTCTTGGGTCATTCGGGTTATC
Found at i:19277 original size:16 final size:15
Alignment explanation
Indices: 19251--19281 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
19241 TGTTTTCTTC
19251 ATATATAATAAATAA
1 ATATATAATAAATAA
19266 ATATATTAATAAATAA
1 ATATA-TAATAAATAA
19282 TTAATTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATATAATAAATAA
Found at i:20851 original size:39 final size:39
Alignment explanation
Indices: 20803--20883 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
20793 GACTTAACAA
20803 AAACTTAACTGAGCATTCTTTACTGTGTTATTGCTTAAT
1 AAACTTAACTGAGCATTCTTTACTGTGTTATTGCTTAAT
* *
20842 AAACTTAACTGAGCATTCTTTATTGTGTTATTGCTTAGT
1 AAACTTAACTGAGCATTCTTTACTGTGTTATTGCTTAAT
20881 AAA
1 AAA
20884 ATCTGGCAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (39 bp):
AAACTTAACTGAGCATTCTTTACTGTGTTATTGCTTAAT
Found at i:23054 original size:1 final size:1
Alignment explanation
Indices: 23048--23076 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
23038 AGATCTTTAT
23048 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23077 GCAAGGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29432 original size:13 final size:13
Alignment explanation
Indices: 29414--29441 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29404 AACGTAGGTT
29414 TGCTCATTCTTCC
1 TGCTCATTCTTCC
29427 TGCTCATTCTTCC
1 TGCTCATTCTTCC
29440 TG
1 TG
29442 TGTGCATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.36, G:0.11, T:0.46
Consensus pattern (13 bp):
TGCTCATTCTTCC
Found at i:31900 original size:9 final size:9
Alignment explanation
Indices: 31884--31915 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31874 TATAAATTAT
31884 TATA-AATA
1 TATATAATA
31892 TATATAATA
1 TATATAATA
31901 TATATAATA
1 TATATAATA
31910 -ATATAA
1 TATATAA
31916 AGAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 10 0.43
9 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TATATAATA
Found at i:37124 original size:19 final size:19
Alignment explanation
Indices: 37074--37124 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
37064 TGTAAGATTT
37074 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
37092 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
37111 TTAATAATTAATTA
1 TTAATAATTAATTA
37125 ATTTCAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:38419 original size:2 final size:2
Alignment explanation
Indices: 38407--38439 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
38397 ATTAATTTCT
*
38407 TA TA AA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38440 AAGCAATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:39185 original size:61 final size:60
Alignment explanation
Indices: 39074--39190 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 60
39064 TCTTAAACCC
* * * *
39074 TAAAATTTAGGAGTAAATATGGGTTAAAATACCCGACAGGTCCCCCTACTTACAAGGGAT
1 TAAAACTTAGGAGCAAATATGGGTTAAAATACCAGACAGGTCCCCATACTTACAAGGGAT
* * *
39134 TAAAACTTAGGAGCAAATATTGGGTTAAAATACACAG-CAGGTCTCTATACTTGCAAG
1 TAAAACTTAGGAGCAAATA-TGGGTTAAAATAC-CAGACAGGTCCCCATACTTACAAG
39191 AAAAAGTCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 17 0.35
61 29 0.60
62 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (60 bp):
TAAAACTTAGGAGCAAATATGGGTTAAAATACCAGACAGGTCCCCATACTTACAAGGGAT
Found at i:39485 original size:18 final size:18
Alignment explanation
Indices: 39449--39490 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
39439 AATTTATTCC
*
39449 TTTTTTTTCAAATTCTAT
1 TTTTTTTTCAAAATCTAT
39467 TTTTGTTTTCAAAAT-TAT
1 TTTT-TTTTCAAAATCTAT
39485 TATTTT
1 T-TTTT
39491 AGTATGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTTTTCAAAATCTAT
Found at i:41803 original size:22 final size:21
Alignment explanation
Indices: 41778--42319 Score: 226
Period size: 22 Copynumber: 25.0 Consensus size: 21
41768 ATTTTTTGTG
41778 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
* *
41800 ACCTTCCTATGAAATTTTAATG
1 ACC-TCCTATGAAATTTTGATA
* * * * * *
41822 ACGATACTATGGAATATCGAGA
1 AC-CTCCTATGAAATTTTGATA
** * **
41844 ACCTTTTTAT-TAATTTTTTTA
1 ACC-TCCTATGAAATTTTGATA
* * *
41865 ACATTCTTATGAAATTTTGTTA
1 AC-CTCCTATGAAATTTTGATA
* *
41887 ACCTCCCTAAGGAATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
41908 GACCTCACTATGAAATTTTGATA
1 -ACCTC-CTATGAAATTTTGATA
* * *
41931 ACCAACACTATGAGATGTTGATA
1 ACC-TC-CTATGAAATTTTGATA
* * *
41954 ACCTCCAAATGATATATTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * * *
41976 ACCACGTTATGAAAATTTAAAA
1 ACCTC-CTATGAAATTTTGATA
41998 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCC-TATGAAATT-TTGA-TA
* * *
42020 ATCACACTCTGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* * * *
42042 ATCACACTATG-AATTGTAATA
1 ACCTC-CTATGAAATTTTGATA
* *
42063 ACCTCGTTATGAAATTTTAATAA
1 ACCTC-CTATGAAATTTTGAT-A
*
42086 ACCTTCCTATAAAATTTTGATAA
1 ACC-TCCTATGAAATTTTGAT-A
*
42109 ACCTCCCTATAAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
*
42131 ACCTCCTTATGAAATCTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
42153 A----CTA-CAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
* **
42169 ATCTCCCTATGATTTTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* *
42191 ACCTCATTATGAAATTTTGTTA
1 ACCTC-CTATGAAATTTTGATA
*
42213 ATCTCCCTATGAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* *
42235 ACCATCTTATGAAATTTTCA-A
1 ACC-TCCTATGAAATTTTGATA
* *
42256 AACTAAACTATGAAATTTTGATA
1 ACCT--CCTATGAAATTTTGATA
*
42279 ACCTTCATATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
* * *
42301 TCCTCC-CTCAAATTTTGAT
1 ACCTCCTATGAAATTTTGAT
42320 TATTTCATAA
Statistics
Matches: 392, Mismatches: 92, Indels: 74
0.70 0.16 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 12 0.03
21 46 0.12
22 246 0.63
23 71 0.18
24 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:42221 original size:44 final size:44
Alignment explanation
Indices: 41872--43071 Score: 226
Period size: 44 Copynumber: 27.9 Consensus size: 44
41862 TTAACATTCT
* * * * * *
41872 TATGAAATTTTGTTAACC-TCCCTAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATAACCAT-CTTATGAAATTTTGATA-ATCTCCC
* * * * * *
41916 TATGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * * * * * * *
41961 AATGATATATTGATAACCA-CGTTATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * *
42005 TATG-AATTGTT-AGTAATCACA-C-TCTGAAATTTTGATAATCACAC
1 TATGAAATT-TTGA-TAA-C-CATCTTATGAAATTTTGATAATCTCCC
* * * * *
42049 TATG-AATTGTAATAACC-TCGTTATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGAT-AATCTCCC
* * * * *
42093 TATAAAATTTTGATAAACC-TCCCTATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGAT-AACCAT-CTTATGAAATTTTGATAATCTCCC
* *
42138 TATGAAATCTTGAT-A--A-C-TA-CAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCTCCC
** *
42176 TATGATTTTTTGATAACC-TCATTATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * **
42220 TATGAAATTTTGATAACCATCTTATGAAATTTTCA-AAACTAAAC
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCT-CCC
* *
42264 TATGAAATTTTGATAACCTTCATATGAAATTTTGAT-ATCCTCCC
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAAT-CTCCC
* * ** * * * * * *
42308 --TCAAATTTTGATTA-TTTCATAATAAAAGTTTAATAACCTTCC
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * *
42350 T-T---A-TTTGGTAACCATATTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCTCCC
* * * **
42389 CA-G-AA-----AT-ACCA-C-TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCTCCC
* *
42423 TTTGAAAATTTGATAACC-TCTTTATGAAATTTTGATAA-C-CCC
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * * * * ** **
42465 TCGATAAAATTTTGTTGACCCTC-TATGAAATTCTGATAATAACAT
1 T--ATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCTCCC
* * *
42510 TATGTAATTTTGATAACC-TCGCTT-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAACCAT--CTTATGAAATTTTGATAATC-TCCC
* * *
42554 TATGAAATTTTGATAATC-TACCTAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAACCAT-CTTATGAAATTTTGATAAT-C--TCCC
* * * **
42600 TATGAAATTTCGATAATCA-CTCTATGAGA-TTTGATAA-CTTTC
1 TATGAAATTTTGATAACCATCT-TATGAAATTTTGATAATCTCCC
* * * * * * * *
42642 TATCAAATTTTGGT-ACTCCTCATGAAATTGAGACTTTT-ATAACCTTCA
1 TATGAAATTTTGATAAC-CATC-T--TA-TGA-AATTTTGATAATCTCCC
* ** * * *
42690 TATGAAATTTTGATAACCA-CACTAAAAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * * * * *
42734 TATGAAATTTTAATAACC-TC-TACGGGATATATT-AGTAACCTCCT
1 TATGAAATTTTGATAACCATCTTA--TGAAATTTTGA-TAATCTCCC
* * *
42778 TATGAAATTTCGTTAACCA-CATTATGAAATTCTT-ATAA-CCCCGC
1 TATGAAATTTTGATAACCATC-TTATGAAATT-TTGATAATCTCC-C
* * * **
42822 TATGACATTTTGAT-A--ATC---T----CTTTGATAACCTTTC
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCTCCC
* * ** * *
42856 TAT-ATAATTGTGATAACCA-CACTATGAAATTTCAATAACCTTCC
1 TATGA-AATTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* * * * * * * * *
42900 TAAGAAATTTTAATAGCCCGATCCTATGAAATTTAGGTAAGCACAC
1 TATGAAATTTTGATA-ACC-ATCTTATGAAATTTTGATAATCTCCC
* * * *
42946 TATGAATTTTTGATAACCTTCTCATGAAATTTTGATAAGT-TCCA
1 TATGAAATTTTGATAACCATCTTATGAAATTTTGATAA-TCTCCC
* * *
42990 TATGAAATTTTTG-TAACCA-CACTATGGAATTTTGATAACCT-CC
1 TATGAAA-TTTTGATAACCATC-TTATGAAATTTTGATAATCTCCC
* *
43033 TCATGAAATTATAATAACCATCTTATGAAATTTTGATAA
1 T-ATGAAATTTTGATAACCATCTTATGAAATTTTGATAA
43072 CCACACAGAG
Statistics
Matches: 837, Mismatches: 213, Indels: 212
0.66 0.17 0.17
Matches are distributed among these distances:
33 3 0.00
34 33 0.04
35 3 0.00
36 7 0.01
37 2 0.00
38 28 0.03
39 27 0.03
40 4 0.00
41 11 0.01
42 52 0.06
43 88 0.11
44 378 0.45
45 84 0.10
46 86 0.10
47 10 0.01
48 19 0.02
49 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACCATCTTATGAAATTTTGATAATCTCCC
Found at i:42540 original size:22 final size:21
Alignment explanation
Indices: 42425--43073 Score: 154
Period size: 22 Copynumber: 29.8 Consensus size: 21
42415 AATCACATTT
* *
42425 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
42447 TGAAATTTTGATAACC-CCTCGA
1 TGAAATTTTGATAACCTCCT--A
* * *
42469 TAAAATTTTGTTGACC-CTCTA
1 TGAAATTTTGATAACCTC-CTA
* *** *
42490 TGAAATTCTGATAATAACATTA
1 TGAAATTTTGATAACCTC-CTA
* *
42512 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTC-CTA
**
42534 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTC-CTA
*
42556 TGAAATTTTGATAATCTACCTA
1 TGAAATTTTGATAACCT-CCTA
42578 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TC-CTA
*
42602 TGAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAA-C-CTCCTA
* * *
42624 TGAGA-TTTGATAACTTTCTA
1 TGAAATTTTGATAACCTCCTA
* *
42644 TCAAATTTTGGT-A-CTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* *
42664 TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAA-T-----TTTGATAACC-TCCTA
*
42692 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
** *
42714 AAAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
42736 TGAAATTTTAATAACCT-CTA
1 TGAAATTTTGATAACCTCCTA
* * *
42756 CGGGATATATT-AGTAACCTCCTTA
1 --TGAAATTTTGA-TAACCTCC-TA
* * * *
42780 TGAAATTTCGTTAACCACATTA
1 TGAAATTTTGATAACCTC-CTA
*
42802 TGAAATTCTT-ATAACCCCGCTA
1 TGAAATT-TTGATAACCTC-CTA
* * *
42824 TGACATTTTGATAATCT-CTT
1 TGAAATTTTGATAACCTCCTA
** *
42844 TGATAACCTT--T---CT-ATA
1 TGA-AATTTTGATAACCTCCTA
* * * *
42860 T-AATTGTGAT-A-ACCAC-ACTA
1 TGAAAT-T-TTGATAAC-CTCCTA
**
42880 TGAAATTTCAATAACCTTCCTA
1 TGAAATTTTGATAACC-TCCTA
* * *
42902 AGAAATTTTAATAGCCCGATCCTA
1 TGAAATTTTGATA-ACC--TCCTA
* * * *
42926 TGAAATTTAGGTAAGCACACTA
1 TGAAATTTTGATAACCTC-CTA
* *
42948 TGAATTTTTGATAACCTTCTCA
1 TGAAATTTTGATAACCTCCT-A
**
42970 TGAAATTTTGATAAGTTCCATA
1 TGAAATTTTGATAACCTCC-TA
*
42992 TGAAATTTTTG-TAACCACACTA
1 TGAAA-TTTTGATAACCTC-CTA
*
43014 TGGAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* * *
43036 TGAAATTATAATAACCATCTTA
1 TGAAATTTTGATAACC-TCCTA
43058 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
43074 ACACAGAGAC
Statistics
Matches: 452, Mismatches: 118, Indels: 114
0.66 0.17 0.17
Matches are distributed among these distances:
14 1 0.00
15 1 0.00
16 5 0.01
19 5 0.01
20 29 0.06
21 59 0.13
22 281 0.62
23 19 0.04
24 22 0.05
25 13 0.03
26 5 0.01
27 2 0.00
28 7 0.02
29 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:42540 original size:65 final size:66
Alignment explanation
Indices: 42444--42570 Score: 148
Period size: 65 Copynumber: 1.9 Consensus size: 66
42434 GATAACCTCT
* * * * *
42444 TTATGAAATTTTGATAACCCCTCGATAAAATTTTGTTGAC-CCTCTATGAAATTCTGATAATAAC
1 TTATGAAATTTTGATAACCCCGCGATAAAATTTTGATAACAACACTATGAAATTCTGATAATAAC
42508 A
66 A
* * ** * *
42509 TTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAAT
1 TTATGAAATTTTGATAACCCCGCGATAAAATTTTGATAACAACACTATGAAATTCTGATAAT
42571 CTACCTATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
65 32 0.64
66 18 0.36
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCCCGCGATAAAATTTTGATAACAACACTATGAAATTCTGATAATAAC
A
Found at i:42562 original size:87 final size:87
Alignment explanation
Indices: 42400--42565 Score: 208
Period size: 87 Copynumber: 1.9 Consensus size: 87
42390 AGAAATACCA
* * * * * **
42400 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCCC
1 CTATGAAATTCTGATAATAACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
*
42465 TCGATAAAATTTTGTTGACCCT
66 ACGATAAAATTTTGTTGACCCT
* *
42487 CTATGAAATTCTGATAATAACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTCTGATAATAACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
* *
42551 CACTATGAAATTTTG
65 CACGATAAAATTTTG
42566 ATAATCTACC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
87 64 0.97
88 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (87 bp):
CTATGAAATTCTGATAATAACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACGATAAAATTTTGTTGACCCT
Found at i:43060 original size:66 final size:66
Alignment explanation
Indices: 42869--43077 Score: 201
Period size: 66 Copynumber: 3.1 Consensus size: 66
42859 ATAATTGTGA
* ** * * *
42869 TAACCACACTATGAAATTTCAATAACCTTCCT-AAGAAATTTTAATAGCCCGATCCTATGAAATT
1 TAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTTTAATA-ACC-ATCATATGAAATT
**
42933 TAGG
63 TTTG
* * * **
42937 TAAGCACACTAT-GAATTTTTGATAACCTTCTCATGAAATTTTGATAA-GTTCCATATGAAATTT
1 TAACCACACTATGGAA-TTTTGATAACCTCCTCATGAAATTTTAATAACCAT-CATATGAAATTT
43000 TTG
64 TTG
* *
43003 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAA-TTTT
1 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTTTAATAACCATCATATGAAATTTTT
43067 G
66 G
43068 ATAACCACAC
1 -TAACCACAC
43078 AGAGACAAGG
Statistics
Matches: 115, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
65 6 0.05
66 68 0.59
67 9 0.08
68 32 0.28
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (66 bp):
TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTTTAATAACCATCATATGAAATTTTT
G
Found at i:43470 original size:13 final size:13
Alignment explanation
Indices: 43452--43479 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43442 TCGTACTTTT
43452 ATATATAGTATAG
1 ATATATAGTATAG
43465 ATATATAGTATAG
1 ATATATAGTATAG
43478 AT
1 AT
43480 TTGGAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
ATATATAGTATAG
Found at i:44327 original size:56 final size:56
Alignment explanation
Indices: 44241--44352 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
44231 GAGTGAGCTT
44241 TGGAAAATTTTAAGTTTAAATGTTTAATATAAAACGTGAACAACAATTGATTCCTA
1 TGGAAAATTTTAAGTTTAAATGTTTAATATAAAACGTGAACAACAATTGATTCCTA
*
44297 TGGAAAATTTTTAGTTTAAATGTTTAATATAAAACGTGAACAACAATTGATTCCTA
1 TGGAAAATTTTAAGTTTAAATGTTTAATATAAAACGTGAACAACAATTGATTCCTA
44353 AAAAAAAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (56 bp):
TGGAAAATTTTAAGTTTAAATGTTTAATATAAAACGTGAACAACAATTGATTCCTA
Found at i:44896 original size:45 final size:45
Alignment explanation
Indices: 44832--44922 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
44822 ATCAATTAAG
44832 TTTTAAATATTTCAATCTAGTCCCTAGAGTACACATATCACCCTT
1 TTTTAAATATTTCAATCTAGTCCCTAGAGTACACATATCACCCTT
44877 TTTTAAATATTTCAATCTAGTCCCTAGAGTACACATATCACCCTT
1 TTTTAAATATTTCAATCTAGTCCCTAGAGTACACATATCACCCTT
44922 T
1 T
44923 AGGACATGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
TTTTAAATATTTCAATCTAGTCCCTAGAGTACACATATCACCCTT
Found at i:45739 original size:18 final size:17
Alignment explanation
Indices: 45718--45770 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
45708 CTTGTGCCTT
*
45718 CCAAACATTCCGTGCTTC
1 CCAAAC-TTCCATGCTTC
*
45736 CCAAACTTCCCATGCTTT
1 CCAAACTT-CCATGCTTC
45754 CCAAACTTCCCATGCTT
1 CCAAACTT-CCATGCTT
45771 AAATTTCCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 2 0.06
18 30 0.94
ACGTcount: A:0.23, C:0.40, G:0.08, T:0.30
Consensus pattern (17 bp):
CCAAACTTCCATGCTTC
Found at i:45780 original size:15 final size:15
Alignment explanation
Indices: 45760--45797 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
45750 CTTTCCAAAC
45760 TTCCCATGCTTAAAT
1 TTCCCATGCTTAAAT
*
45775 TTCCCATGTTTAAAT
1 TTCCCATGCTTAAAT
*
45790 TTTCCATG
1 TTCCCATG
45798 ACCATGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.45
Consensus pattern (15 bp):
TTCCCATGCTTAAAT
Found at i:46378 original size:33 final size:33
Alignment explanation
Indices: 46332--46420 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
46322 ACTATGAGGT
* * * *
46332 GGATATGCTGCTGGAGGGTATCCTCCTGG-GGGA
1 GGATATCCAGCTGGAGGGTATCCGCC-GGCAGGA
46365 GGATATCCAGCTGGAGGGTATCCGCCGGCAGGA
1 GGATATCCAGCTGGAGGGTATCCGCCGGCAGGA
* *
46398 GGATAACCAGCAGGAGGGTATCC
1 GGATATCCAGCTGGAGGGTATCC
46421 AGCTGGTGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.21, C:0.21, G:0.39, T:0.18
Consensus pattern (33 bp):
GGATATCCAGCTGGAGGGTATCCGCCGGCAGGA
Found at i:46386 original size:15 final size:15
Alignment explanation
Indices: 46362--46432 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
46352 TCCTCCTGGG
*
46362 GGAGGATATCCAGCT
1 GGAGGGTATCCAGCT
*
46377 GGAGGGTATCC-GCC
1 GGAGGGTATCCAGCT
* *
46391 GGCAGGAGGATAACCAGCA
1 GG-A-G-GG-TATCCAGCT
46410 GGAGGGTATCCAGCT
1 GGAGGGTATCCAGCT
*
46425 GGTGGGTA
1 GGAGGGTA
46433 GCCTTGTGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
14 4 0.09
15 25 0.57
16 3 0.07
17 3 0.07
18 5 0.11
19 4 0.09
ACGTcount: A:0.24, C:0.20, G:0.41, T:0.15
Consensus pattern (15 bp):
GGAGGGTATCCAGCT
Found at i:51627 original size:13 final size:13
Alignment explanation
Indices: 51609--51647 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
51599 TTACCTGTTA
51609 GATATATGCAAAT
1 GATATATGCAAAT
51622 GATATATGCAAAT
1 GATATATGCAAAT
51635 GATATATGCAAAT
1 GATATATGCAAAT
51648 TTTGTTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
GATATATGCAAAT
Found at i:56194 original size:11 final size:11
Alignment explanation
Indices: 56180--56205 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56170 ATAGAAATCA
56180 AATATAAACTC
1 AATATAAACTC
56191 AATATAAACTC
1 AATATAAACTC
56202 AATA
1 AATA
56206 CATAAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATAAACTC
Done.