Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021814.1 Corchorus olitorius cultivar O-4 contig21847, 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: 44788
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6850 original size:15 final size:15
Alignment explanation
Indices: 6830--6859 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6820 TTTCCTTTGG
6830 TTCTCAATTTTTCAA
1 TTCTCAATTTTTCAA
6845 TTCTCAATTTTTCAA
1 TTCTCAATTTTTCAA
6860 AGATGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCTCAATTTTTCAA
Found at i:10655 original size:26 final size:26
Alignment explanation
Indices: 10623--10673 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
10613 TATGTGTTTG
* *
10623 AAAGGTTGTTGATAATATTCACAAAA
1 AAAGGTTGTTGATAAAATTAACAAAA
*
10649 AAAGGTTGTTGGTAAAATTAACAAA
1 AAAGGTTGTTGATAAAATTAACAAA
10674 GTATGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (26 bp):
AAAGGTTGTTGATAAAATTAACAAAA
Found at i:17251 original size:11 final size:11
Alignment explanation
Indices: 17230--17271 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
17220 GTTTTTCTAT
17230 TTTTTGTTTTTG
1 TTTTTG-TTTTG
17242 TTTTTGTTTTG
1 TTTTTGTTTTG
* *
17253 TTTTCGTTTTT
1 TTTTTGTTTTG
17264 TTTTTGTT
1 TTTTTGTT
17272 GCGGTGTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 21 0.78
12 6 0.22
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.83
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:17253 original size:17 final size:17
Alignment explanation
Indices: 17231--17271 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
17221 TTTTTCTATT
*
17231 TTTTGTTTTTGTTTTTG
1 TTTTGTTTTCGTTTTTG
*
17248 TTTTGTTTTCGTTTTTT
1 TTTTGTTTTCGTTTTTG
17265 TTTTGTT
1 TTTTGTT
17272 GCGGTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (17 bp):
TTTTGTTTTCGTTTTTG
Found at i:20040 original size:6 final size:6
Alignment explanation
Indices: 20029--20061 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
20019 GAGCTATCAA
20029 AAACCC AAACCC AAACCC AAACCC AAACCC AAA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAA
20062 GCATGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:21248 original size:21 final size:21
Alignment explanation
Indices: 21222--21261 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21212 AATTGTGAAA
*
21222 AAGTTGATGAAGAAAAAGAGG
1 AAGTTGAAGAAGAAAAAGAGG
*
21243 AAGTTGAAGAAGAATAAGA
1 AAGTTGAAGAAGAAAAAGA
21262 ATAAGAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (21 bp):
AAGTTGAAGAAGAAAAAGAGG
Found at i:35034 original size:2 final size:2
Alignment explanation
Indices: 35027--35066 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
35017 TATAATTTTA
35027 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
35067 GATGTAGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39886 original size:22 final size:21
Alignment explanation
Indices: 39791--40161 Score: 123
Period size: 22 Copynumber: 16.9 Consensus size: 21
39781 TAAAAATACC
* *
39791 ACTATGAAATTTTGGTAATCAC
1 ACTATGAAATTTTGATAA-CAT
* * * *
39813 ATTTTGAAAATTTGATAACCT
1 ACTATGAAATTTTGATAACAT
*
39834 -CTTTATGAAATTTTGATAACCT
1 AC--TATGAAATTTTGATAACAT
*
39856 -CGTTTTGAAATTTTGATAACAAT
1 AC--TATGAAATTTTGATAAC-AT
*
39879 ACTATGAAATTTTGATAATCTT
1 ACTATGAAATTTTGATAA-CAT
*
39901 CCTAT-AAATTTTGATAATTCGAT
1 ACTATGAAATTTTGATAA--C-AT
*
39924 ATTTATGAAATTTTGATAATCACT
1 A-CTATGAAATTTTGATAA-CA-T
* * *
39948 -TTATGAGA-TTTGATAACCT
1 ACTATGAAATTTTGATAACAT
* * * *
39967 TCTATCAAATTTTGGTACTCAT
1 ACTATGAAATTTTGATA-ACAT
* *
39989 GA-AATTGAGACTTTT-ATAATC-T
1 -ACTA-TGA-AATTTTGATAA-CAT
* *
40011 TCATATGAAATTTTGATAACCAC
1 AC-TATGAAATTTTGATAA-CAT
*
40034 ACTATGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAA-CAT
*
40056 ACTATGAAATTTTGATAACCT
1 ACTATGAAATTTTGATAACAT
* * * * *
40077 CCCCATGATATATT-AGTAACCT
1 -ACTATGAAATTTTGA-TAACAT
* * *
40099 CCTTATGAAATTTTGTTAACCAC
1 AC-TATGAAATTTTGATAA-CAT
40122 ACTATGAAATTCTT-ATAACAT
1 ACTATGAAATT-TTGATAACAT
* *
40143 CGCTATGACATTTTGATAA
1 -ACTATGAAATTTTGATAA
40162 TCCCTTTGAT
Statistics
Matches: 265, Mismatches: 55, Indels: 58
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.00
20 6 0.02
21 40 0.15
22 179 0.68
23 15 0.06
24 12 0.05
25 12 0.05
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ACTATGAAATTTTGATAACAT
Found at i:40024 original size:21 final size:22
Alignment explanation
Indices: 40014--40161 Score: 151
Period size: 22 Copynumber: 6.7 Consensus size: 22
40004 ATAATCTTCA
40014 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
40036 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
40058 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * * *
40080 CATGATATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
40101 TTATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
*
40124 TATGAAATTCTT-ATAA-CATCGC
1 TATGAAATT-TTGATAACCA-CAC
*
40146 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
40162 TCCCTTTGAT
Statistics
Matches: 106, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
21 6 0.06
22 97 0.92
23 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:40150 original size:44 final size:42
Alignment explanation
Indices: 39792--40377 Score: 180
Period size: 44 Copynumber: 13.5 Consensus size: 42
39782 AAAAATACCA
* * * * * *
39792 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTC
1 CTATGAAATTTTGATAACCACACTATG-AAATTTTATAACATC
* * ** * *
39835 TTTATGAAATTTTGATAACCTCGTTTTGAAATTTTGATAACAATA
1 -CTATGAAATTTTGATAACCACACTATGAAATTTT-ATAAC-ATC
** *
39880 CTATGAAATTTTGATAATCTTC-CTAT-AAATTTTGATAATTCGATAT
1 CTATGAAATTTTGATAA-CCACACTATGAAATTTT-ATAA--C-AT-C
* * ** * * * *
39926 TTATGAAATTTTGATAATCACTTTATGAGATTTGATAACCTT
1 CTATGAAATTTTGATAACCACACTATGAAATTTTATAACATC
* * * * * *
39968 CTATCAAATTTTGGT-ACTCATGA-AATTGAGACTTTTATAATCTTC
1 CTATGAAATTTTGATAAC-CA-CACTA-TGA-AATTTTATAA-CATC
*
40013 ATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCA-C
1 CTATGAAATTTTGATAACCACACTATGAAATTTT-ATAA-CATC
* * * * * *
40056 ACTATGAAATTTTGATAACCTCCCCATGATATATTAGTAACCTC
1 -CTATGAAATTTTGATAACCACACTATGAAATTTTA-TAACATC
*
40100 CTTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACATC
1 C-TATGAAATTTTGATAACCACACTATGAAATT-TTATAACATC
* * *
40144 GCTATGACATTTTGATAATC-C-CTTTGATAACTTTT-T----T-
1 -CTATGAAATTTTGATAACCACACTATGA-AA-TTTTATAACATC
* * * * *
40181 -TATAAAATTGTGATAACCGCACTATGAAATTTCAATAACCTTC
1 CTATGAAATTTTGATAACCACACTATGAAATTT-TATAA-CATC
* * * **
40224 CTAAGAAATTTTAATAACTTGATC-CTATGAAAATTTGGTAACCA-C
1 CTATGAAATTTTGATAAC--CA-CACTATG-AAATTTTATAA-CATC
*** *
40269 ACTATGAAATTTTGATAACC-TTTTCATGAAATTTTGATAACTTC
1 -CTATGAAATTTTGATAACCACACT-ATGAAATTTT-ATAACATC
* * * *
40313 CATATGAAATTTTGGTAACCACACTATGGAATTTTGACAACCTC
1 C-TATGAAATTTTGATAACCACACTATGAAATTTT-ATAACATC
* *
40357 CTCATGAAATTATAATAACCA
1 CT-ATGAAATTTTGATAACCA
40378 TCTTATGAAA
Statistics
Matches: 402, Mismatches: 93, Indels: 94
0.68 0.16 0.16
Matches are distributed among these distances:
35 17 0.04
36 3 0.01
37 6 0.01
38 1 0.00
41 1 0.00
42 23 0.06
43 46 0.11
44 211 0.52
45 31 0.08
46 51 0.13
47 12 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (42 bp):
CTATGAAATTTTGATAACCACACTATGAAATTTTATAACATC
Found at i:40255 original size:24 final size:22
Alignment explanation
Indices: 40202--40324 Score: 65
Period size: 22 Copynumber: 5.5 Consensus size: 22
40192 GATAACCGCA
40202 CTATGAAATTTCAATAACCTTC
1 CTATGAAATTTCAATAACCTTC
* * *
40224 CTAAGAAATTTTAATAACTTGATC
1 CTATGAAATTTCAATAACCT--TC
** *
40248 CTATGAAAATTT-GGTAACC-AC
1 CTATG-AAATTTCAATAACCTTC
**
40269 ACTATGAAATTTTGATAACCTT-
1 -CTATGAAATTTCAATAACCTTC
* **
40291 TTCATGAAATTTTGATAA-CTTC
1 CT-ATGAAATTTCAATAACCTTC
40313 CATATGAAATTT
1 C-TATGAAATTT
40325 TGGTAACCAC
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
21 11 0.14
22 52 0.65
23 1 0.01
24 10 0.12
25 6 0.08
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTCAATAACCTTC
Found at i:40276 original size:22 final size:21
Alignment explanation
Indices: 40248--40376 Score: 91
Period size: 22 Copynumber: 5.9 Consensus size: 21
40238 TAACTTGATC
* *
40248 CTATGAAAATTTGGTAACCACA
1 CTATGAAATTTTGATAACC-CA
**
40270 CTATGAAATTTTGATAACCTT
1 CTATGAAATTTTGATAACCCA
*
40291 TTCATGAAATTTTGATAACTTCCA
1 CT-ATGAAATTTTGATAAC--CCA
*
40315 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACC-CA
* *
40336 CTATGGAATTTTGACAACCTC-
1 CTATGAAATTTTGATAACC-CA
* *
40357 CTCATGAAATTATAATAACC
1 CT-ATGAAATTTTGATAACC
40377 ATCTTATGAA
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 77 0.91
23 1 0.01
24 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCCA
Found at i:40375 original size:66 final size:66
Alignment explanation
Indices: 40184--40375 Score: 199
Period size: 66 Copynumber: 2.9 Consensus size: 66
40174 CTTTTTTTAT
* * ** * * *
40184 AAAATTGTGATAACCGCACTATGAAATTTCAATAACCTTCCT-AAGAAATTTTAATAACTTGATC
1 AAAATT-TGGTAACCACACTATGAAATTTTGACAACC-TCCTCATGAAATTATAATAAC-T--TC
40248 C-TATG
61 CATATG
* ** * *
40253 AAAATTTGGTAACCACACTATGAAATTTTGATAACCTTTTCATGAAATTTTGATAACTTCCATAT
1 AAAATTTGGTAACCACACTATGAAATTTTGACAACCTCCTCATGAAATTATAATAACTTCCATAT
40318 G
66 G
* *
40319 AAATTTTGGTAACCACACTATGGAATTTTGACAACCTCCTCATGAAATTATAATAAC
1 AAAATTTGGTAACCACACTATGAAATTTTGACAACCTCCTCATGAAATTATAATAAC
40376 CATCTTATGA
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
65 3 0.03
66 54 0.51
67 3 0.03
68 40 0.38
69 6 0.06
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (66 bp):
AAAATTTGGTAACCACACTATGAAATTTTGACAACCTCCTCATGAAATTATAATAACTTCCATAT
G
Found at i:40385 original size:66 final size:66
Alignment explanation
Indices: 40185--40402 Score: 190
Period size: 66 Copynumber: 3.3 Consensus size: 66
40175 TTTTTTTATA
* * * ** * * *
40185 AAATTGTGATAACCGCACTATGAAATTTCAATAACCTTCCT-AAGAAATTTTAATAACTTGATCC
1 AAATTTTGGTAACCACACTATGAAATTTTGACAACC-TCCTCATGAAATTATAATAAC---ATCC
40249 -TATG
62 ATATG
* * ** * * *
40253 AAAATTTGGTAACCACACTATGAAATTTTGATAACCTTTTCATGAAATTTTGATAACTTCCATAT
1 AAATTTTGGTAACCACACTATGAAATTTTGACAACCTCCTCATGAAATTATAATAACATCCATAT
40318 G
66 G
* *
40319 AAATTTTGGTAACCACACTATGGAATTTTGACAACCTCCTCATGAAATTATAATAACCAT-CTTA
1 AAATTTTGGTAACCACACTATGAAATTTTGACAACCTCCTCATGAAATTATAATAA-CATCCATA
40383 TG
65 TG
* **
40385 AAATCTTATTAACCACAC
1 AAATTTTGGTAACCACAC
40403 AGAGACAAGA
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
65 3 0.02
66 73 0.59
67 4 0.03
68 44 0.35
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (66 bp):
AAATTTTGGTAACCACACTATGAAATTTTGACAACCTCCTCATGAAATTATAATAACATCCATAT
G
Found at i:40602 original size:20 final size:20
Alignment explanation
Indices: 40564--40602 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40554 TATTGACATT
40564 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
40584 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
40603 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:41893 original size:19 final size:19
Alignment explanation
Indices: 41869--41908 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
41859 AAGTCTTATC
41869 AATGGAGAAAATATACTTT
1 AATGGAGAAAATATACTTT
41888 AATGGAGAAAATATACTTT
1 AATGGAGAAAATATACTTT
41907 AA
1 AA
41909 GAAAAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (19 bp):
AATGGAGAAAATATACTTT
Found at i:42337 original size:35 final size:35
Alignment explanation
Indices: 42291--42361 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
42281 TGAGGTACGT
42291 TTTCACTCTCTAACGCCTACACACGCTCAAAACCC
1 TTTCACTCTCTAACGCCTACACACGCTCAAAACCC
*
42326 TTTCACTCTCTAACGCCTACACACGTTCAAAACCC
1 TTTCACTCTCTAACGCCTACACACGCTCAAAACCC
42361 T
1 T
42362 AGATATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.41, G:0.06, T:0.25
Consensus pattern (35 bp):
TTTCACTCTCTAACGCCTACACACGCTCAAAACCC
Found at i:43809 original size:22 final size:21
Alignment explanation
Indices: 43753--43905 Score: 126
Period size: 22 Copynumber: 7.0 Consensus size: 21
43743 GTCACTGTGT
*
43753 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
43774 TTGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
43797 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
43819 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
43841 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
* *
43863 GGTCATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
** *
43885 GGTTGCCAAACTTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
43906 TCAAGTTATT
Statistics
Matches: 102, Mismatches: 24, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
21 5 0.05
22 92 0.90
23 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:43855 original size:66 final size:66
Alignment explanation
Indices: 43749--43923 Score: 201
Period size: 66 Copynumber: 2.6 Consensus size: 66
43739 TCTTGTCACT
* * * * *
43749 GTGTGGTTATCAAAATTTCATAAGATTGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATG-GGAAGGTCATCAAAATTCCA
43813 TA
65 TA
* *
43815 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGGAAGGTCATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGGAAGGTCATCAAAATTCCA
43879 TA
65 TA
* * * *
43881 GTGTGGTTGCCAAACTTTCATAGGATCAAGTTATTAAAATTTC
1 GTGTGGTTACCAAAATTTCATAAGAT--AGTTATCAAAATTTC
43924 TTAGAAAGGT
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
65 5 0.05
66 73 0.78
67 2 0.02
68 14 0.15
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGGAAGGTCATCAAAATTCCAT
A
Found at i:43943 original size:68 final size:66
Alignment explanation
Indices: 43749--43966 Score: 199
Period size: 66 Copynumber: 3.3 Consensus size: 66
43739 TCTTGTCACT
* * * * * * *
43749 GTGTGGTTATCAAAATTTCATA-AGATTGTTATTATAATTTCAT-GAGGAGGTTATCAAAATTCC
1 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATAGA-AAGGTTATCAAAATTTC
43812 ATA
64 ATA
* * *
43815 GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATGGGAAGGTCATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCAT
43880 A
66 A
* * * * **
43881 GTGTGGTTGCCAAACTTTCATA-GGATCAAGTTATTAAAATTTCTTAGAAAGGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATATGG---AAGTTATCAAAATTTCATAGAAAGGTTATCAAAATTT
43945 CATA
63 CATA
* * *
43949 GTCTGGTTATCACAATTT
1 GTGTGGTTACCAAAATTT
43967 TATAAAAAGG
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
65 2 0.02
66 72 0.58
67 3 0.02
68 47 0.38
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCAT
A
Found at i:44025 original size:22 final size:21
Alignment explanation
Indices: 43989--44150 Score: 103
Period size: 22 Copynumber: 7.4 Consensus size: 21
43979 ATCAAAGAGA
* *
43989 TTATCAAAATGTCATAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
44011 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
*
44033 TTAACAAAATTTCATAAG-GAGG
1 TT-ATAAAATTTCAT-AGTGAGG
* * *
44055 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
*
44077 TTATCAAAATTTCATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
** ** **
44099 TTATCAATTTTTTTTAGTTTGG
1 TTAT-AAAATTTCATAGTGAGG
44121 TTATCAAAATTTCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
44143 TTATAAAA
1 TTATAAAA
44151 GTCTCATTTT
Statistics
Matches: 110, Mismatches: 23, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
21 10 0.09
22 95 0.86
23 5 0.05
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.39
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:44282 original size:22 final size:22
Alignment explanation
Indices: 44255--44408 Score: 89
Period size: 22 Copynumber: 7.0 Consensus size: 22
44245 TTTATAGGAA
*
44255 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAATG-T
* **
44278 G-TTATCAAAGTTAGATAATGT
1 GATTATCAAAATTTCATAATGT
* *
44299 GATTATCAAAATTTCATGGA-GG
1 GATTATCAAAATTTCAT-AATGT
* * * * *
44321 GGTCAGT-AAAATTTTATAAAGAG
1 GATTA-TCAAAATTTCATAATG-T
* * *
44344 GTTTATCAAAATTTCATAAAGA
1 GATTATCAAAATTTCATAATGT
* * *
44366 GGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAATGT
*
44388 GATTACCAAAATTTCATAATG
1 GATTATCAAAATTTCATAATG
44409 GTATTTCTGG
Statistics
Matches: 99, Mismatches: 26, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
21 3 0.03
22 76 0.77
23 20 0.20
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:44356 original size:23 final size:22
Alignment explanation
Indices: 44328--44379 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
44318 AGGGGTCAGT
44328 AAAATTTTATAAAGAGGTTTATC
1 AAAATTTTATAAAGAGG-TTATC
*
44351 AAAATTTCATAAAGAGGTTATC
1 AAAATTTTATAAAGAGGTTATC
44373 -AAATTTT
1 AAAATTTT
44380 CAAAATGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 6 0.22
22 5 0.19
23 16 0.59
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (22 bp):
AAAATTTTATAAAGAGGTTATC
Found at i:44781 original size:22 final size:21
Alignment explanation
Indices: 44421--44781 Score: 217
Period size: 22 Copynumber: 17.0 Consensus size: 21
44411 ATTTCTGGGA
*
44421 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGG
*
44442 ATGGTTA-CCAAA--T--TAGG
1 A-GGTTATCAAAATTTCATAGG
* * *
44459 AAGGTTATTAAACTTTTATTATGG
1 -AGGTTATCAAAATTTCA-TA-GG
* *
44483 A-GTAATCAAAATTTCA-GGG
1 AGGTTATCAAAATTTCATAGG
* *
44502 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GG
* *
44524 AGGTTATCAGAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG--G
* *
44547 A-GTTTTCAAAATTTCATAAG
1 AGGTTATCAAAATTTCATAGG
* *
44567 AGGGTTAGCAAAATTTCATAGT
1 A-GGTTATCAAAATTTCATAGG
* *
44589 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATA-GG
** * *
44612 AGAATAACAAAATTTCATAATG
1 AGGTTATCAAAATTTCAT-AGG
**
44634 AGGTTATCAAAAAATCATAAGG
1 AGGTTATCAAAATTTCAT-AGG
*
44656 AGGTTATCAAAA-TT--T-GT
1 AGGTTATCAAAATTTCATAGG
*
44673 A-GTTATCAAGATTTCATAAGG
1 AGGTTATCAAAATTTCAT-AGG
*
44694 AGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATA-GG
*
44716 AGGTTTATCAAAATTTTATAGG
1 AGG-TTATCAAAATTTCATAGG
44738 AAGGTTTATCAAAATTTCATAGCG
1 -AGG-TTATCAAAATTTCATAG-G
*
44762 AGGTTATCACAATTTCATAG
1 AGGTTATCAAAATTTCATAG
44782 TGTGATT
Statistics
Matches: 262, Mismatches: 49, Indels: 57
0.71 0.13 0.15
Matches are distributed among these distances:
16 9 0.03
17 12 0.05
18 3 0.01
19 6 0.02
20 15 0.06
21 12 0.05
22 156 0.60
23 46 0.18
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGG
Done.