Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015838.1 Corchorus capsularis cultivar CVL-1 contig15859, 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: 40049
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:124 original size:33 final size:31
Alignment explanation
Indices: 87--193 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 31
77 GCCGCCCCAG
*
87 TGGGGCGACTTACCATGGCTCAAGCCGCCCTCC
1 TGGGGCGGCTTACCATGG-T-AAGCCGCCCTCC
* *
120 TGGGGCGGCTCTGCCA-CGTGAAGCCGCCCTCC
1 TGGGGCGGCT-TACCATGGT-AAGCCGCCCTCC
*
152 TAGGGCGGCTTGAGCCATGGTAAGCCGCCCTCC
1 TGGGGCGGCTT-A-CCATGGTAAGCCGCCCTCC
185 TGGGGCGGC
1 TGGGGCGGC
194 ACGGGTCATC
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 22 0.35
33 33 0.53
34 6 0.10
ACGTcount: A:0.12, C:0.36, G:0.35, T:0.17
Consensus pattern (31 bp):
TGGGGCGGCTTACCATGGTAAGCCGCCCTCC
Found at i:10575 original size:12 final size:12
Alignment explanation
Indices: 10558--10627 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
10548 AGGAAAATCC
10558 CGTTCCTGAAGT
1 CGTTCCTGAAGT
10570 CGTTCCT-AATGT
1 CGTTCCTGAA-GT
* *
10582 TGTTCTTGAAGT
1 CGTTCCTGAAGT
* *
10594 CGATCCTGTAGT
1 CGTTCCTGAAGT
10606 CGTTCCTGAAGT
1 CGTTCCTGAAGT
*
10618 TGTTCCTGAA
1 CGTTCCTGAA
10628 CCCCAAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (12 bp):
CGTTCCTGAAGT
Found at i:13917 original size:32 final size:32
Alignment explanation
Indices: 13860--14062 Score: 221
Period size: 32 Copynumber: 6.2 Consensus size: 32
13850 TATTGACTCC
* * *
13860 ACTTAATTA-CTTGAACTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTCCTTTATTCT
* *
13891 TCTTAATTACCCTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTCCTTTATTCT
**
13923 ACTTAATTACCCTGAATTAAACCCTTTATTGACTCT
1 ACTTAATTACCCTGAATTAAGTCCTTTA-T---TCT
* *
13959 ACTTAATTACCCTAAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTCCTTTATTCT
* *
13991 ACTTAATTACCCTGAATTAAGTCCCTGATT-T
1 ACTTAATTACCCTGAATTAAGTCCTTTATTCT
* * *
14022 GACTTAACTACCCTGAATTAAGTCCTTGACTCT
1 -ACTTAATTACCCTGAATTAAGTCCTTTATTCT
14055 ACTTAATT
1 ACTTAATT
14063 TCTTTCCTTG
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
31 9 0.06
32 107 0.73
33 2 0.01
35 1 0.01
36 27 0.18
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCCTTTATTCT
Found at i:14003 original size:100 final size:99
Alignment explanation
Indices: 13847--14042 Score: 286
Period size: 100 Copynumber: 2.0 Consensus size: 99
13837 AGATTAAGTT
* * *
13847 CTTTATTGACTCCACTTAATTACTTGAACTAAGTTCTTTATTCTTCTTAATTACCCTGAATTAAG
1 CTTTATTGACTCCACTTAATTACCTAAACTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAG
* * * *
13912 TTCTTTATTCT-ACTTAATTACCCTGAATTAAACC
66 TCCCTGATT-TGACTTAACTACCCTGAATTAAACC
* *
13946 CTTTATTGACTCTACTTAATTACCCTAAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
1 CTTTATTGACTCCACTTAATTA-CCTAAACTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
14011 GTCCCTGATTTGACTTAACTACCCTGAATTAA
65 GTCCCTGATTTGACTTAACTACCCTGAATTAA
14043 GTCCTTGACT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 22 0.26
100 64 0.74
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (99 bp):
CTTTATTGACTCCACTTAATTACCTAAACTAAGTTCTTTATTCTACTTAATTACCCTGAATTAAG
TCCCTGATTTGACTTAACTACCCTGAATTAAACC
Found at i:14088 original size:37 final size:37
Alignment explanation
Indices: 14037--14189 Score: 195
Period size: 37 Copynumber: 4.2 Consensus size: 37
14027 AACTACCCTG
*
14037 AATTAAGTCCTTGACTCTACTTAATTTCTTTCCTTGA
1 AATTAAGTCATTGACTCTACTTAATTTCTTTCCTTGA
* * *
14074 AATTACGTCATTGACTCTATTTAATTTCCTTCCTTGA
1 AATTAAGTCATTGACTCTACTTAATTTCTTTCCTTGA
*
14111 AATTAAGTCATTGACTCTACTTAA-TTCTCTTCCTCGA
1 AATTAAGTCATTGACTCTACTTAATTTCT-TTCCTTGA
* * * *
14148 AATTAAGTCCTTAACTCTACTTAATTCCCTT-C-TGA
1 AATTAAGTCATTGACTCTACTTAATTTCTTTCCTTGA
14183 AATTAAG
1 AATTAAG
14190 CCCTCTTCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
35 9 0.09
36 4 0.04
37 86 0.85
38 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.42
Consensus pattern (37 bp):
AATTAAGTCATTGACTCTACTTAATTTCTTTCCTTGA
Found at i:14240 original size:36 final size:36
Alignment explanation
Indices: 14199--14336 Score: 106
Period size: 36 Copynumber: 3.9 Consensus size: 36
14189 GCCCTCTTCT
* * *
14199 TTACTTAGTC-CCCTTAGGTTAAGTTTTTGTCTGATC
1 TTACTTAATCACCCTTAGATTAAGTCTTTG-CTGATC
* * *
14235 TTACTTAATCATCTTTAGATTAAGTCTTTGCTGATT
1 TTACTTAATCACCCTTAGATTAAGTCTTTGCTGATC
* * *
14271 TTACTTAAT--TCTTGTGAAATTAAGTCTTTGCTGAT-
1 TTACTTAATCACCCT-T-AGATTAAGTCTTTGCTGATC
* * *
14306 TTACTTAATTACCCTGA-ATTAAGTCTGTGCT
1 TTACTTAATCACCCTTAGATTAAGTCTTTGCT
14337 TGTCTTTACC
Statistics
Matches: 86, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
34 17 0.20
35 11 0.13
36 41 0.48
37 17 0.20
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (36 bp):
TTACTTAATCACCCTTAGATTAAGTCTTTGCTGATC
Found at i:14331 original size:34 final size:34
Alignment explanation
Indices: 14217--14336 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 34
14207 TCCCCTTAGG
* * * * *
14217 TTAAGTTTTTGTCTGATCTTACTTAATCATCTTTAGA
1 TTAAGTCTTTG-CTGAT-TTACTTAATTACCCTGA-A
**
14254 TTAAGTCTTTGCTGATTTTACTTAATT-CTTGTGAAA
1 TTAAGTCTTTGCTGA-TTTACTTAATTAC-CCTG-AA
14290 TTAAGTCTTTGCTGATTTACTTAATTACCCTGAA
1 TTAAGTCTTTGCTGATTTACTTAATTACCCTGAA
*
14324 TTAAGTCTGTGCT
1 TTAAGTCTTTGCT
14337 TGTCTTTACC
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
34 14 0.20
35 13 0.19
36 31 0.44
37 12 0.17
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.48
Consensus pattern (34 bp):
TTAAGTCTTTGCTGATTTACTTAATTACCCTGAA
Found at i:14345 original size:71 final size:73
Alignment explanation
Indices: 14217--14351 Score: 161
Period size: 71 Copynumber: 1.9 Consensus size: 73
14207 TCCCCTTAGG
* * * * * *
14217 TTAAGTTTTTGTCTGATCTTACTTAATCATCTTTAGATTAAGTCTTTGCTGATTTTACTTAATTC
1 TTAAGTCTTTGTCTGATCTTACTTAATCACCCTGAGATTAAGTCTGTGCTGATTTTACCTAATTC
14282 TTGTGAAA
66 TTGTGAAA
*
14290 TTAAGTCTTTG-CTGAT-TTACTTAATTACCCTGA-ATTAAGTCTGTGCTTG-TCTTTACCTAAT
1 TTAAGTCTTTGTCTGATCTTACTTAATCACCCTGAGATTAAGTCTGTGC-TGAT-TTTACCTAAT
14351 T
64 T
14352 TCCTTCCTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
70 13 0.25
71 25 0.47
72 5 0.09
73 10 0.19
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.49
Consensus pattern (73 bp):
TTAAGTCTTTGTCTGATCTTACTTAATCACCCTGAGATTAAGTCTGTGCTGATTTTACCTAATTC
TTGTGAAA
Found at i:14351 original size:36 final size:39
Alignment explanation
Indices: 14285--14501 Score: 180
Period size: 41 Copynumber: 5.5 Consensus size: 39
14275 TTAATTCTTG
* * *
14285 TGAAATTAAGTCTTTGC-TG-ATTTACTTAATTAC-CC-
1 TGAAATTAAGTCTGTGCTTGTCTTTACCTAATTACTCCT
*
14320 TG-AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCT
1 TGAAATTAAGTCTGTGCTTGTCTTTACCTAA-TTAC-TCCT
*
14360 TGAAATTAAG-CATGTGCTTGTCTTTACCTAATTTCCTTCCT
1 TGAAATTAAGTC-TGTGCTTGTCTTTACCTAA-TTAC-TCCT
* * *
14401 TGAAATTAAGTCCGTGCTT-TACTTAACCTAATTTCCTTCCT
1 TGAAATTAAGTCTGTGCTTGT-CTTTACCTAA-TTAC-TCCT
* *
14442 TGAAATTAAGTCTGTACTT-TACTTTACCTAATTTCCTTCCT
1 TGAAATTAAGTCTGTGCTTGT-CTTTACCTAA-TTAC-TCCT
*
14483 TAAAATTAAGTCTGTGCTT
1 TGAAATTAAGTCTGTGCTT
14502 TACTGTTTTT
Statistics
Matches: 161, Mismatches: 11, Indels: 14
0.87 0.06 0.08
Matches are distributed among these distances:
34 13 0.08
35 4 0.02
36 8 0.05
37 3 0.02
39 2 0.01
40 4 0.02
41 126 0.78
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (39 bp):
TGAAATTAAGTCTGTGCTTGTCTTTACCTAATTACTCCT
Found at i:14368 original size:41 final size:41
Alignment explanation
Indices: 14322--14505 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 41
14312 AATTACCCTG
14322 AATTAAGTCTGTGCTTGT-CTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTT-TACTTTACCTAATTTCCTTCCTTGA
14363 AATTAAG-CATGTGCTTGT-CTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTC-TGTGCTT-TACTTTACCTAATTTCCTTCCTTGA
* *
14404 AATTAAGTCCGTGCTTTACTTAACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
* *
14445 AATTAAGTCTGTACTTTACTTTACCTAATTTCCTTCCTTAA
1 AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
14486 AATTAAGTCTGTGCTTTACT
1 AATTAAGTCTGTGCTTTACT
14506 GTTTTTACTT
Statistics
Matches: 133, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
40 2 0.02
41 130 0.98
42 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (41 bp):
AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
Found at i:14549 original size:40 final size:40
Alignment explanation
Indices: 14502--14612 Score: 186
Period size: 40 Copynumber: 2.8 Consensus size: 40
14492 GTCTGTGCTT
*
14502 TACTGTTTTTACTTAATTTCCATGAATTAAGTCCTTTGAC
1 TACTGTTTTTACTTAATTTCCATGAATTAAGTCCTTTAAC
*
14542 TATTGTTTTTACTTAATTTCCATGAATTAAGTCCTTTAAC
1 TACTGTTTTTACTTAATTTCCATGAATTAAGTCCTTTAAC
* *
14582 TGCTGTTTTTACTTAATTTCTATGAATTAAG
1 TACTGTTTTTACTTAATTTCCATGAATTAAG
14613 CCCCTGACTG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (40 bp):
TACTGTTTTTACTTAATTTCCATGAATTAAGTCCTTTAAC
Found at i:14682 original size:70 final size:69
Alignment explanation
Indices: 14606--14861 Score: 364
Period size: 70 Copynumber: 3.8 Consensus size: 69
14596 AATTTCTATG
* * * * * *
14606 AATTAAGCCCCTGACTGTGCTTACTCTTCTTAATTACCCTGGATTAAAACTTTGCTTTTCTTAAT
1 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTG-TTTTCTTAAT
*
14671 TACTA
65 TACCA
*
14676 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGAC---G-TTGC-T--TT
1 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGTTTTCTTAATT
14734 ACCA
66 ACCA
*
14738 AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGTTTTTCTTAAT
1 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTG-TTTTCTTAAT
14803 TACCA
65 TACCA
14808 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTG
1 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTG
14862 ATTGTGTTTA
Statistics
Matches: 167, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
62 54 0.32
64 1 0.01
65 4 0.02
67 4 0.02
68 1 0.01
70 103 0.62
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (69 bp):
AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGTTTTCTTAATT
ACCA
Found at i:14711 original size:31 final size:31
Alignment explanation
Indices: 14676--14773 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
14666 TTAATTACTA
14676 AATTAAGACCTTGACTATGCTTACTTTTCTT
1 AATTAAGACCTTGACTATGCTTACTTTTCTT
* * * * * **
14707 AATT---ACCCTGAATTAAGACGTTGCTTTACCA
1 AATTAAGACCTTG-ACTATG-C-TTACTTTTCTT
*
14738 AATTAAGACCTTGACTATTCTTACTTTTCTT
1 AATTAAGACCTTGACTATGCTTACTTTTCTT
14769 AATTA
1 AATTA
14774 CCCTGAATTA
Statistics
Matches: 46, Mismatches: 15, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
28 5 0.11
29 4 0.09
30 1 0.02
31 27 0.59
32 1 0.02
33 3 0.07
34 5 0.11
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (31 bp):
AATTAAGACCTTGACTATGCTTACTTTTCTT
Found at i:14787 original size:41 final size:41
Alignment explanation
Indices: 14738--14862 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
14728 TGCTTTACCA
14738 AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTG
1 AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTG
* *
14779 AATT-A-A----GACT-TT-GT--TTTTCTTAATTA-CC-A
1 AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTG
*
14808 AATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTG
1 AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTG
*
14849 AATTAAGACTTTGA
1 AATTAAGACCTTGA
14863 TTGTGTTTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
29 4 0.06
30 3 0.05
31 13 0.20
33 1 0.02
34 2 0.03
35 8 0.12
36 1 0.02
37 1 0.02
39 13 0.20
40 3 0.05
41 17 0.26
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (41 bp):
AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTG
Found at i:14843 original size:132 final size:132
Alignment explanation
Indices: 14606--14857 Score: 423
Period size: 132 Copynumber: 1.9 Consensus size: 132
14596 AATTTCTATG
* * *
14606 AATTAAGCCCCTGACTGTGCTTACTCTTCTTAATTACCCTGGATTAAAACTTTGCTTTTCTTAAT
1 AATTAAGACCCTGACTATGCTTACTCTTCTTAATTACCCTGAATTAAAACTTTGCTTTTCTTAAT
*
14671 TACTAAATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACGTTGCTTTAC
66 TACCAAATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACGTTGCTTTAC
14736 CA
131 CA
* * * * *
14738 AATTAAGACCTTGACTATTCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGTTTTTCTTAAT
1 AATTAAGACCCTGACTATGCTTACTCTTCTTAATTACCCTGAATTAAAACTTTGCTTTTCTTAAT
14803 TACCAAATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGAC
66 TACCAAATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGAC
14858 TTTGATTGTG
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
132 111 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (132 bp):
AATTAAGACCCTGACTATGCTTACTCTTCTTAATTACCCTGAATTAAAACTTTGCTTTTCTTAAT
TACCAAATTAAGACCTTGACTATGCTTACTTTTCTTAATTACCCTGAATTAAGACGTTGCTTTAC
CA
Found at i:14928 original size:60 final size:60
Alignment explanation
Indices: 14828--14954 Score: 200
Period size: 60 Copynumber: 2.1 Consensus size: 60
14818 TTGACTATGC
* *
14828 TTACTTTTCTTAATTACCCTGAATTAAGACTTTGATTGTGTTTACCTCCTTTAACTGTGT
1 TTACCTTTCTTAATTACCCTGAATTAAGACTTTGACTGTGTTTACCTCCTTTAACTGTGT
* * * *
14888 TTACCTTTCTTAATTACCCTTAATTAAGACTTTGACTGTGTTTACTTTCTTTCACTGTGT
1 TTACCTTTCTTAATTACCCTGAATTAAGACTTTGACTGTGTTTACCTCCTTTAACTGTGT
14948 TTACCTT
1 TTACCTT
14955 ATTTAACTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (60 bp):
TTACCTTTCTTAATTACCCTGAATTAAGACTTTGACTGTGTTTACCTCCTTTAACTGTGT
Found at i:14944 original size:19 final size:19
Alignment explanation
Indices: 14917--14973 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
14907 TTAATTAAGA
*
14917 CTTTGACTGTGTTTACTTT
1 CTTTAACTGTGTTTACTTT
* *
14936 CTTTCACTGTGTTTACCTT
1 CTTTAACTGTGTTTACTTT
*
14955 ATTTAACTGTGTTTACTTT
1 CTTTAACTGTGTTTACTTT
14974 TCTTAATTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.14, C:0.18, G:0.12, T:0.56
Consensus pattern (19 bp):
CTTTAACTGTGTTTACTTT
Found at i:14962 original size:79 final size:78
Alignment explanation
Indices: 14864--15009 Score: 247
Period size: 79 Copynumber: 1.9 Consensus size: 78
14854 AGACTTTGAT
* *
14864 TGTGTTTACCTCCTTTAACTGTGTTTACCTTTCTTAATTACCCTTAATTAAGACTTTGACTGTGT
1 TGTGTTTACCTCATTTAACTGTGTTTACCTTTCTTAATTACCCTGAATTAAGACTTT-ACTGTGT
14929 TTACTTTCTTTCAC
65 TTACTTTCTTTCAC
* *
14943 TGTGTTTACCTTATTTAACTGTGTTTACTTTTCTTAATTACCCTGAATTAAGACTTTACTGTGTT
1 TGTGTTTACCTCATTTAACTGTGTTTACCTTTCTTAATTACCCTGAATTAAGACTTTACTGTGTT
15008 TA
66 TA
15010 TGGTTGCATA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 10 0.16
79 53 0.84
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (78 bp):
TGTGTTTACCTCATTTAACTGTGTTTACCTTTCTTAATTACCCTGAATTAAGACTTTACTGTGTT
TACTTTCTTTCAC
Found at i:14979 original size:19 final size:19
Alignment explanation
Indices: 14922--14979 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
14912 TAAGACTTTG
*
14922 ACTGTGTTTAC-TTTCTTTC
1 ACTGTGTTTACTTTTC-TTA
*
14941 ACTGTGTTTACCTTAT-TTA
1 ACTGTGTTTA-CTTTTCTTA
14960 ACTGTGTTTACTTTTCTTA
1 ACTGTGTTTACTTTTCTTA
14979 A
1 A
14980 TTACCCTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 26 0.79
20 1 0.03
21 2 0.06
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (19 bp):
ACTGTGTTTACTTTTCTTA
Found at i:17755 original size:6 final size:6
Alignment explanation
Indices: 17744--17789 Score: 58
Period size: 7 Copynumber: 7.3 Consensus size: 6
17734 AATTATAAAC
17744 TTCTTT TTC-TT TTCTTT TTCTTTT TTCTTTT TTCTTT TTCCTTT TT
1 TTCTTT TTCTTT TTCTTT TTC-TTT TTC-TTT TTCTTT TT-CTTT TT
17790 TTCTCTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 13 0.35
7 19 0.51
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTCTTT
Found at i:17770 original size:7 final size:7
Alignment explanation
Indices: 17753--17790 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
17743 CTTCTTTTTC
17753 TTTTC-T
1 TTTTCTT
17759 TTTTCTT
1 TTTTCTT
17766 TTTTCTT
1 TTTTCTT
17773 TTTTCTT
1 TTTTCTT
*
17780 TTTCCTT
1 TTTTCTT
17787 TTTT
1 TTTT
17791 TCTCTTCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:17798 original size:20 final size:19
Alignment explanation
Indices: 17747--17799 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
17737 TATAAACTTC
17747 TTTTTCTTTTCTTTTTCTT
1 TTTTTCTTTTCTTTTTCTT
*
17766 TTTTCTTTTTTCTTTTTCCTT
1 TTTT-TCTTTTCTTTTT-CTT
*
17787 TTTTTCTCTTCTT
1 TTTTTCTTTTCTT
17800 AAAGGATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 7 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTCTT
Found at i:20453 original size:30 final size:30
Alignment explanation
Indices: 20397--20461 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
20387 CATCTACTCA
* * *
20397 AGAAAGATAAATGACATCAGAGAACATTTT
1 AGAAAGATAAATGAAATCACAGAACATTAT
* *
20427 AGAAAGATAAATGAAATTACATAACATTAT
1 AGAAAGATAAATGAAATCACAGAACATTAT
20457 AGAAA
1 AGAAA
20462 TAAGTGAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.23
Consensus pattern (30 bp):
AGAAAGATAAATGAAATCACAGAACATTAT
Found at i:27274 original size:20 final size:20
Alignment explanation
Indices: 27251--27295 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
27241 CCTTAAATCT
27251 CAAATCTCTCCTGTAAACCC
1 CAAATCTCTCCTGTAAACCC
*
27271 CAAATCTCTCTTGTAAACCC
1 CAAATCTCTCCTGTAAACCC
27291 CAAAT
1 CAAAT
27296 TCAAAGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (20 bp):
CAAATCTCTCCTGTAAACCC
Found at i:29555 original size:62 final size:62
Alignment explanation
Indices: 29484--29605 Score: 235
Period size: 62 Copynumber: 2.0 Consensus size: 62
29474 TGTTCGAACT
29484 CATCTAGATGATATGAAGACCATCGAAGTTCAATTGAAGAGTTTTGCTGATGATTTCGGCGA
1 CATCTAGATGATATGAAGACCATCGAAGTTCAATTGAAGAGTTTTGCTGATGATTTCGGCGA
*
29546 CATCTAGATGATATGAAGACCATCGAAGTTCAATTGAAGAGTTTTGGTGATGATTTCGGC
1 CATCTAGATGATATGAAGACCATCGAAGTTCAATTGAAGAGTTTTGCTGATGATTTCGGC
29606 AAGAAGACTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (62 bp):
CATCTAGATGATATGAAGACCATCGAAGTTCAATTGAAGAGTTTTGCTGATGATTTCGGCGA
Found at i:34359 original size:20 final size:20
Alignment explanation
Indices: 34343--34383 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34333 AAATCAAAGT
*
34343 AAAACCAAGATAATCAATCC
1 AAAACCAAGATAATCAAACC
* *
34363 AAAACCAAGATTATAAAACC
1 AAAACCAAGATAATCAAACC
34383 A
1 A
34384 GATCAGTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.22, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAACCAAGATAATCAAACC
Found at i:37556 original size:31 final size:33
Alignment explanation
Indices: 37521--37587 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 33
37511 GTATAATTTG
37521 AAACTAA-TTCATTTATATA-ATATATATATAT
1 AAACTAATTTCATTTATATATATATATATATAT
*
37552 AAACTAATTCTTCATTTATATATATATTTATATAT
1 AAACTAA-T-TTCATTTATATATATATATATATAT
37587 A
1 A
37588 TTCAATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
34 12 0.39
35 12 0.39
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (33 bp):
AAACTAATTTCATTTATATATATATATATATAT
Done.