Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007032.1 Corchorus capsularis cultivar CVL-1 contig07053, 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: 64162
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:997 original size:22 final size:23
Alignment explanation
Indices: 969--1090 Score: 87
Period size: 22 Copynumber: 5.3 Consensus size: 23
959 GGAAGAATTT
969 AAATTGAAGCATTGACATG-TTG
1 AAATTGAAGCATTGACATGATTG
* *
991 AAATTGAAACATTGGCAT--TTGG
1 AAATTGAAGCATTGACATGATT-G
* * *
1013 AATTTGAAGAATTGAAATTGAATTG
1 AAATTGAAGCATTGACA-TG-ATTG
*
1038 AAATTTAAGCATTGA-A-GAATTG
1 AAATTGAAGCATTGACATG-ATTG
1060 AAATTGAAGCATTGA-A-GAATTG
1 AAATTGAAGCATTGACATG-ATTG
1082 AAAATTGAA
1 -AAATTGAA
1091 ATTGAAGCGT
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.02
22 56 0.67
23 9 0.11
24 1 0.01
25 13 0.16
26 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.31
Consensus pattern (23 bp):
AAATTGAAGCATTGACATGATTG
Found at i:1033 original size:6 final size:6
Alignment explanation
Indices: 1022--1096 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
1012 GAATTTGAAG
*
1022 AATTGA AATTG- AATTGA AATTTA AGCATTGAA GAATTGA AATTGA AGCATTGAA
1 AATTGA AATTGA AATTGA AATTGA A--ATTG-A -AATTGA AATTGA A--ATTG-A
1076 GAATTGAA AATTGA AATTGA A
1 -AATTG-A AATTGA AATTGA A
1097 GCGTCAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
5 5 0.09
6 26 0.45
7 6 0.10
8 17 0.29
9 2 0.03
10 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.31
Consensus pattern (6 bp):
AATTGA
Found at i:1061 original size:8 final size:8
Alignment explanation
Indices: 1016--1169 Score: 65
Period size: 8 Copynumber: 20.0 Consensus size: 8
1006 CATTTGGAAT
1016 TTGAAGAA
1 TTGAAGAA
1024 TTG-A-AA
1 TTGAAGAA
1030 TTGAATTGAAA
1 TTGAA--G-AA
* *
1041 TTTAAGCA
1 TTGAAGAA
1049 TTGAAGAA
1 TTGAAGAA
1057 TTG-A-AA
1 TTGAAGAA
*
1063 TTGAAGCA
1 TTGAAGAA
1071 TTGAAGAA
1 TTGAAGAA
1079 TTGAA-AA
1 TTGAAGAA
1086 TTG-A-AA
1 TTGAAGAA
**
1092 TTGAAGCG
1 TTGAAGAA
** *
1100 TCAAAGAT
1 TTGAAGAA
1108 TTG-A-AA
1 TTGAAGAA
* * *
1114 TCGAGGTA
1 TTGAAGAA
*
1122 TTGAATAA
1 TTGAAGAA
*
1130 TTGAGGAA
1 TTGAAGAA
* *
1138 ATGAAGTA
1 TTGAAGAA
*
1146 TTGAATAA
1 TTGAAGAA
*
1154 TTAAAGAA
1 TTGAAGAA
1162 TTGAAGAA
1 TTGAAGAA
1170 AGAGATCATT
Statistics
Matches: 102, Mismatches: 33, Indels: 22
0.65 0.21 0.14
Matches are distributed among these distances:
6 19 0.19
7 11 0.11
8 65 0.64
9 1 0.01
11 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.29
Consensus pattern (8 bp):
TTGAAGAA
Found at i:1065 original size:14 final size:14
Alignment explanation
Indices: 910--1097 Score: 82
Period size: 14 Copynumber: 12.4 Consensus size: 14
900 GAAGGAGGCT
910 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
924 TTGAA-ACATTGAAACTGAA
1 TTGAAGA-ATTG--A---AA
943 TTCGAAGAATTGAAA
1 TT-GAAGAATTGAAA
* *
958 TGGAAGAATTTAAA
1 TTGAAGAATTGAAA
* *
972 TTGAAGCATTGACATG
1 TTGAAGAATTGA-A-A
988 TTG-A-AATTGAAACA
1 TTGAAGAATTG-AA-A
* *
1002 TTG--GCATTTGGAAT
1 TTGAAG-AATT-GAAA
1016 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
1030 TTGAATTGAAATTTAAGCA
1 TTGAA--G-AATTGAA--A
1049 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
1063 TTGAAGCATTGAAGAA
1 TTGAAGAATTG-A-AA
1079 TTGAA-AATTGAAA
1 TTGAAGAATTGAAA
1092 TTGAAG
1 TTGAAG
1098 CGTCAAAGAT
Statistics
Matches: 133, Mismatches: 17, Indels: 48
0.67 0.09 0.24
Matches are distributed among these distances:
13 8 0.06
14 60 0.45
15 19 0.14
16 20 0.15
17 7 0.05
18 1 0.01
19 10 0.08
20 7 0.05
21 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:1106 original size:29 final size:29
Alignment explanation
Indices: 1019--1113 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
1009 TTGGAATTTG
**
1019 AAGAATTG-AAATTG-AATTGAA--ATTT
1 AAGAATTGAAAATTGAAATTGAAGCATCA
* **
1044 AAGCATTGAAGAATTGAAATTGAAGCATTG
1 AAGAATTGAA-AATTGAAATTGAAGCATCA
*
1074 AAGAATTGAAAATTGAAATTGAAGCGTCA
1 AAGAATTGAAAATTGAAATTGAAGCATCA
*
1103 AAGATTTGAAA
1 AAGAATTGAAA
1114 TCGAGGTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
25 7 0.12
26 1 0.02
27 5 0.09
28 7 0.12
29 26 0.45
30 12 0.21
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.28
Consensus pattern (29 bp):
AAGAATTGAAAATTGAAATTGAAGCATCA
Found at i:1112 original size:51 final size:51
Alignment explanation
Indices: 1033--1133 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
1023 ATTGAAATTG
* ** *
1033 AATTGAAATTTAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAA
1 AATTGAAATTGAAGCATCAAAGAATTGAAATCGAAGCATTGAAGAATTGAA
* * * * *
1084 AATTGAAATTGAAGCGTCAAAGATTTGAAATCGAGGTATTGAATAATTGA
1 AATTGAAATTGAAGCATCAAAGAATTGAAATCGAAGCATTGAAGAATTGA
1134 GGAAATGAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.30
Consensus pattern (51 bp):
AATTGAAATTGAAGCATCAAAGAATTGAAATCGAAGCATTGAAGAATTGAA
Found at i:2982 original size:12 final size:13
Alignment explanation
Indices: 2940--2989 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
2930 CATGATTCTC
2940 TTTTGAAAAACATT
1 TTTTGAAAAACA-T
2954 TTTTGAAGAAAACA-
1 TTTTG-A-AAAACAT
*
2968 TTTTGAAAAATAT
1 TTTTGAAAAACAT
2981 TTTTGAAAA
1 TTTTGAAAA
2990 CCATGACCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 5 0.16
13 10 0.31
14 10 0.31
15 1 0.03
16 6 0.19
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAACAT
Found at i:2991 original size:61 final size:64
Alignment explanation
Indices: 2918--3040 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 64
2908 TTTTTGTGTT
* *
2918 TTTTCTGAAAACCATGA-TTCTCTTTTGAAAAACATTTTTTGAAGAAAA-CA-TTTTGAAAAATA
1 TTTTCTGAAAACCATGACTTCTCTTTTAAAAAACA-TTTTTGAAAAAAAGCATTTTTGAAAAATA
* *
2980 TTTT-TGAAAACCATGACCTTTTTTTTTAAAAAACATTTTTGAAAAAAAGCATTTTTGAAAA
1 TTTTCTGAAAACCATGA-CTTCTCTTTTAAAAAACATTTTTGAAAAAAAGCATTTTTGAAAA
3041 CCATGACTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
61 12 0.23
62 16 0.30
63 16 0.30
64 9 0.17
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.40
Consensus pattern (64 bp):
TTTTCTGAAAACCATGACTTCTCTTTTAAAAAACATTTTTGAAAAAAAGCATTTTTGAAAAATA
Found at i:3025 original size:15 final size:16
Alignment explanation
Indices: 3007--3040 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2997 CTTTTTTTTT
3007 AAAAAA-CATTTTTGA
1 AAAAAAGCATTTTTGA
3022 AAAAAAGCATTTTTGA
1 AAAAAAGCATTTTTGA
3038 AAA
1 AAA
3041 CCATGACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (16 bp):
AAAAAAGCATTTTTGA
Found at i:3409 original size:2 final size:2
Alignment explanation
Indices: 3359--3393 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3349 GAACAGCAGA
3359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3394 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10833 original size:20 final size:17
Alignment explanation
Indices: 10799--10859 Score: 86
Period size: 17 Copynumber: 3.4 Consensus size: 17
10789 GGTGTCTAAA
10799 AAGCGCAACCATGTTGG
1 AAGCGCAACCATGTTGG
*
10816 AAGCGTCAGCATCATGTTGG
1 AAGCG-CA--ACCATGTTGG
10836 AAGCGCAACCATGTTGG
1 AAGCGCAACCATGTTGG
10853 AAGCGCA
1 AAGCGCA
10860 TATGAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 21 0.54
18 2 0.05
19 2 0.05
20 14 0.36
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.18
Consensus pattern (17 bp):
AAGCGCAACCATGTTGG
Found at i:10913 original size:45 final size:45
Alignment explanation
Indices: 10843--10959 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
10833 TGGAAGCGCA
* ** *
10843 ACCATGTTGGAAGCGCATATGAATTTTATCG-CTGGAAGCGCCACC
1 ACCATGTTGGAAGAGTGTATAAATTTTAT-GACTGGAAGCGCCACC
* * *
10888 -CTCATGTTGGAAGAGTGTATAAATTTTGTGATTGGAGGCGCCACC
1 AC-CATGTTGGAAGAGTGTATAAATTTTATGACTGGAAGCGCCACC
10933 ACCATGTTGGAAGCA-TGTATAAATTTT
1 ACCATGTTGGAAG-AGTGTATAAATTTT
10960 GACAATTTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
44 2 0.03
45 57 0.93
46 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (45 bp):
ACCATGTTGGAAGAGTGTATAAATTTTATGACTGGAAGCGCCACC
Found at i:10960 original size:45 final size:45
Alignment explanation
Indices: 10875--10960 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
10865 ATTTTATCGC
10875 TGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAAATTTTGTGAT
1 TGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAAATTTTGTGAT
*
10920 TGGAGGCGCCACCAC-CATGTTGGAAGCA-TGTATAAATTTTG
1 TGGAAGCGCCACC-CTCATGTTGGAAG-AGTGTATAAATTTTG
10961 ACAATTTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (45 bp):
TGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAAATTTTGTGAT
Found at i:11717 original size:42 final size:40
Alignment explanation
Indices: 11546--11719 Score: 158
Period size: 40 Copynumber: 4.4 Consensus size: 40
11536 GGGCATTGTA
* * * *
11546 AAGCTGCAAAGGCTGTAGGCATAGTAAGCCTTTT-TTTTT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
* * * * * *
11585 AAAGCTGCATAAGCTATAGGCGTTGTACGCC--CTC-TTTC
1 -AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
*
11623 AAGCTACATTGGCTATAGGCATTGTAAGCCTTTTCTTTTT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
* * *
11663 AAGCTTCATAGGCTATATGCATTGTAAGCCTTTTTTTTTTTT
1 AAGCTACATAGGCTATAGGCATTGTAAGCC--TTTTCTTTTT
*
11705 AAGCTGCATAGGCTA
1 AAGCTACATAGGCTA
11720 GAAGTGTCAA
Statistics
Matches: 108, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
37 25 0.23
38 4 0.04
39 2 0.02
40 54 0.50
42 23 0.21
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
AAGCTACATAGGCTATAGGCATTGTAAGCCTTTTCTTTTT
Found at i:11825 original size:110 final size:112
Alignment explanation
Indices: 11696--11965 Score: 365
Period size: 110 Copynumber: 2.5 Consensus size: 112
11686 GTAAGCCTTT
* * *
11696 TTTTTTTTTAA---GCTGCATAGGCTAGAAGT-GTCAACAAGGAGGGGCACTCCTGGAGGTGCAA
1 TTTTTTTTTAATGGGCTACATAGGCCAGAA-TCGTCAACAAGGAAGGGCACTCCTGGAGGTGCAA
* * *
11757 TCAGTGCAACACTCCTAAGGGTGCAC-CTGCTCCAAGTCAAAATATA-A
65 CCAATGCAACACTCCTAAGGGTGCACTC-ACTCCAAGTCAAAATATAGA
*
11804 -TTTTTTTTAATGGGCTACATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAAC
1 TTTTTTTTTAATGGGCTACATAGGCCAGAATCGTCAACAAGGAAGGGCACTCCTGGAGGTGCAAC
* * * *
11868 CAATGCAGCACTCTTATGGGTGCACTCACTCCAAGTTAAAATATAGA
66 CAATGCAACACTCCTAAGGGTGCACTCACTCCAAGTCAAAATATAGA
*
11915 TTTTTTTTTAATGGGCTACATAGGCCAGAATCGTCAACAAGGAAAGGCACT
1 TTTTTTTTTAATGGGCTACATAGGCCAGAATCGTCAACAAGGAAGGGCACT
11966 TATGGCTACG
Statistics
Matches: 142, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
107 10 0.07
109 1 0.01
110 81 0.57
111 2 0.01
112 48 0.34
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (112 bp):
TTTTTTTTTAATGGGCTACATAGGCCAGAATCGTCAACAAGGAAGGGCACTCCTGGAGGTGCAAC
CAATGCAACACTCCTAAGGGTGCACTCACTCCAAGTCAAAATATAGA
Found at i:13035 original size:46 final size:46
Alignment explanation
Indices: 12966--13054 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
12956 GTGTCACTGT
*
12966 TTTAAGGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATCTGA
1 TTTAAAGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATCTGA
* *
13012 TTTAAAGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATC
1 TTTAAAGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATC
13055 AAGGAAGATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (46 bp):
TTTAAAGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATCTGA
Found at i:13998 original size:2 final size:2
Alignment explanation
Indices: 13991--14025 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13981 CCGGTTAGCC
13991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14026 GAGGTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16446 original size:2 final size:2
Alignment explanation
Indices: 16425--16474 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
16415 TATTCTATTT
* *
16425 TC TC CC TC TA TC TAC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16468 TC TC TC T
1 TC TC TC T
16475 GGTTCACGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.04, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:18684 original size:30 final size:30
Alignment explanation
Indices: 18650--18741 Score: 87
Period size: 33 Copynumber: 3.0 Consensus size: 30
18640 CATGCGACAT
*
18650 CGCATGGAGCAACCGGCCACAACCAGCCAA
1 CGCATGGAGCAACCGGCCACAACCGGCCAA
* * *
18680 CGCATGAAGCACCAACTGGCCACAACCGGCCAT
1 CGCATG--G-AGCAACCGGCCACAACCGGCCAA
* *
18713 CGCATGG-GCCATCCGGGCACAACCGGCCA
1 CGCATGGAG-CAACCGGCCACAACCGGCCA
18742 TTTGATCCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
30 23 0.46
31 1 0.02
32 1 0.02
33 25 0.50
ACGTcount: A:0.28, C:0.40, G:0.25, T:0.07
Consensus pattern (30 bp):
CGCATGGAGCAACCGGCCACAACCGGCCAA
Found at i:26602 original size:2 final size:2
Alignment explanation
Indices: 26583--26635 Score: 70
Period size: 2 Copynumber: 25.5 Consensus size: 2
26573 ATTAAAAATA
* *
26583 AT AT AT AGT AT AT TT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26626 AT GAT AT AT A
1 AT -AT AT AT A
26636 AAATGATTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 41 0.91
3 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:27131 original size:33 final size:32
Alignment explanation
Indices: 27089--27195 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 32
27079 TACCGTGGCG
27089 AAGCCGCCCCACTGGGGAGGCTCAACCACGGGA
1 AAGCCGCCCCACTGGGGAGGCTC-ACCACGGGA
* * *
27122 AAGCCGCCCCACTGGGGCGGCTTCACCATGGGC
1 AAGCCGCCCCACTGGGGAGGC-TCACCACGGGA
* * * *
27155 AGGCCGCCCCACTGGGGTGGCTTCGCCAC-GGC
1 AAGCCGCCCCACTGGGGAGGC-TCACCACGGGA
27187 AAGCCGCCC
1 AAGCCGCCC
27196 TTATGGGGCG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
32 11 0.17
33 52 0.80
34 2 0.03
ACGTcount: A:0.17, C:0.40, G:0.34, T:0.09
Consensus pattern (32 bp):
AAGCCGCCCCACTGGGGAGGCTCACCACGGGA
Found at i:36313 original size:17 final size:17
Alignment explanation
Indices: 36291--36323 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36281 TTACAGTCCT
36291 CTTTTT-TTCTTTTTTTC
1 CTTTTTCTT-TTTTTTTC
36308 CTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
36324 TATTTACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTCTTTTTTTTTC
Found at i:36322 original size:19 final size:19
Alignment explanation
Indices: 36287--36324 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
36277 TATTTTACAG
36287 TCCTCTTTTTTTCTTTTTT
1 TCCTCTTTTTTTCTTTTTT
36306 TCCT-TTTTCTTT-TTTTTT
1 TCCTCTTTT-TTTCTTTTTT
36324 T
1 T
36325 ATTTACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TCCTCTTTTTTTCTTTTTT
Found at i:37522 original size:5 final size:5
Alignment explanation
Indices: 37513--37547 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
37503 TGAGAATTTA
* *
37513 AAAAA AAAAA AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
37548 TTGAGTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:38337 original size:109 final size:109
Alignment explanation
Indices: 38136--38353 Score: 384
Period size: 109 Copynumber: 2.0 Consensus size: 109
38126 TACTAAGACC
38136 TATACCTATGGAGCCTTTAATAAATCATCTCTCGAATAATGTTCTCCTTGAATCTTGAATATTGT
1 TATACCTATGGAGCCTTTAATAAATCATCTCTCGAATAATGTTCTCCTTGAATCTTGAATATTGT
*
38201 AGCCACAAGTTGTAGAAGCCCAAATTTATCCTAAATTTGAAATA
66 AGCCACAAGTTGTAGAACCCCAAATTTATCCTAAATTTGAAATA
*
38245 TATACCTATGGAGCCTTTAATAAATTC-TCTCTCGAATAATGTTCTCCTTGAATCTTGAATTTTG
1 TATACCTATGGAGCCTTTAATAAA-TCATCTCTCGAATAATGTTCTCCTTGAATCTTGAATATTG
* *
38309 TAGCCACAAGTTGTAGAACCCCATATTTATCCTAAATTTGGAATA
65 TAGCCACAAGTTGTAGAACCCCAAATTTATCCTAAATTTGAAATA
38354 CCAGGATAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
109 102 0.98
110 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (109 bp):
TATACCTATGGAGCCTTTAATAAATCATCTCTCGAATAATGTTCTCCTTGAATCTTGAATATTGT
AGCCACAAGTTGTAGAACCCCAAATTTATCCTAAATTTGAAATA
Found at i:47090 original size:4 final size:4
Alignment explanation
Indices: 47071--47105 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
47061 TGTTACTTAT
47071 TTTA TTCTA TTTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TT-TA -TTTA TTTA TTTA TTTA TTTA TTTA T
47106 AAGAAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 23 0.79
5 4 0.14
6 2 0.07
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:47605 original size:20 final size:19
Alignment explanation
Indices: 47580--47619 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
47570 ATTCAGTCAG
*
47580 TTTTTTAAGTTAGTTCAGTT
1 TTTTTTAAGTCAGTT-AGTT
*
47600 TTTTTTTAGTCAGTTAGTT
1 TTTTTTAAGTCAGTTAGTT
47619 T
1 T
47620 GAGTCTGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.62
Consensus pattern (19 bp):
TTTTTTAAGTCAGTTAGTT
Found at i:47761 original size:27 final size:27
Alignment explanation
Indices: 47731--47786 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
47721 ATGATTCTCG
47731 AATCAGCCACTTTCTTTTTGCTGTTGA
1 AATCAGCCACTTTCTTTTTGCTGTTGA
47758 AATCAGCCACTTTCTTTTTGCTGTTGA
1 AATCAGCCACTTTCTTTTTGCTGTTGA
47785 AA
1 AA
47787 GTTTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (27 bp):
AATCAGCCACTTTCTTTTTGCTGTTGA
Found at i:58333 original size:19 final size:21
Alignment explanation
Indices: 58297--58338 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
58287 TTTCTTCTAT
58297 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
58317 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
58337 TT
1 TT
58339 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:61073 original size:28 final size:28
Alignment explanation
Indices: 61042--61133 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 28
61032 ACTAGCCTAC
*
61042 TTCAAGTGTTGACCACAGATTGGTCTCT
1 TTCAAGTGTTGACCACGGATTGGTCTCT
* * * *
61070 TTCAAATATCAGTTGGCCACGGACTGGCCTAC-
1 TTC-AA-GT--GTTGACCACGGATTGGTCT-CT
*
61102 TTAAAGTGTTGACCACGGATTGGTCTCT
1 TTCAAGTGTTGACCACGGATTGGTCTCT
61130 TTCA
1 TTCA
61134 GGTATTAGTT
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
27 1 0.02
28 22 0.47
29 2 0.04
30 2 0.04
31 2 0.04
32 17 0.36
33 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (28 bp):
TTCAAGTGTTGACCACGGATTGGTCTCT
Found at i:61109 original size:60 final size:60
Alignment explanation
Indices: 61016--61174 Score: 246
Period size: 60 Copynumber: 2.6 Consensus size: 60
61006 CGTCCCAAGG
61016 TATCAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAA
1 TATCAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAA
* * * * * **
61076 TATCAGTTGGCCACGGACTGGCCTACTTAAAGTGTTGACCACGGATTGGTCTCTTTCAGG
1 TATCAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAA
*
61136 TATTAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGAC
1 TATCAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGAC
61175 AATAGCCTAC
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 87 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (60 bp):
TATCAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAA
Found at i:61184 original size:23 final size:23
Alignment explanation
Indices: 61154--61197 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
61144 GGCTACAGAC
*
61154 TAGCCTACTTCAAGTGTTGACAA
1 TAGCCTACTTCAAGTATTGACAA
61177 TAGCCTACTTCAAGTATTGAC
1 TAGCCTACTTCAAGTATTGAC
61198 CACGGATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (23 bp):
TAGCCTACTTCAAGTATTGACAA
Found at i:61243 original size:83 final size:83
Alignment explanation
Indices: 61096--61257 Score: 252
Period size: 83 Copynumber: 2.0 Consensus size: 83
61086 CCACGGACTG
* * * *
61096 GCCTACTTAAAGTGTTGACCACGGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGACTAGCCTA
1 GCCTACTTAAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACAGACTAGCCTA
*
61161 CTTCAAGTGTTGACAATA
66 CTTCAAGTATTGACAATA
* * *
61179 GCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCCTA
1 GCCTACTTAAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACAGACTAGCCTA
61244 CTTCAAGTATTGAC
66 CTTCAAGTATTGAC
61258 CACAGATTGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (83 bp):
GCCTACTTAAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACAGACTAGCCTA
CTTCAAGTATTGACAATA
Found at i:61249 original size:32 final size:31
Alignment explanation
Indices: 61179--61368 Score: 98
Period size: 32 Copynumber: 6.3 Consensus size: 31
61169 GTTGACAATA
* *
61179 GCCTACTTCAAG--TA-TTGACCACGGATTG
1 GCCTACTTCAAGTATAGTTGGCCACGGACTG
*
61207 GTCT-CTTTCAAGTATCAGTTGGCCACGGACTG
1 GCCTAC-TTCAAGTAT-AGTTGGCCACGGACTG
* * *
61239 GCCTACTTCAAG--TA-TTGACCACAGATTG
1 GCCTACTTCAAGTATAGTTGGCCACGGACTG
* * * * *
61267 GTCT-CTTTCAGGTATTAGTTGGCTACAGACTA
1 GCCTAC-TTCAAGTA-TAGTTGGCCACGGACTG
* **
61299 GCCTACTTCAAG--T-GTTGACCACGGGTTG
1 GCCTACTTCAAGTATAGTTGGCCACGGACTG
* *
61327 GTCT-CATTCAAGTATCAGTTGGCTACGGACTG
1 GCCTAC-TTCAAGTAT-AGTTGGCCACGGACTG
61359 GCCTACTTCA
1 GCCTACTTCA
61369 GTGTCGACCA
Statistics
Matches: 117, Mismatches: 27, Indels: 32
0.66 0.15 0.18
Matches are distributed among these distances:
27 3 0.03
28 46 0.39
29 2 0.02
30 3 0.03
31 3 0.03
32 57 0.49
33 3 0.03
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (31 bp):
GCCTACTTCAAGTATAGTTGGCCACGGACTG
Found at i:61272 original size:60 final size:60
Alignment explanation
Indices: 61177--61439 Score: 321
Period size: 60 Copynumber: 4.4 Consensus size: 60
61167 GTGTTGACAA
* * *
61177 TAGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACGGAC
1 TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAGTATCAGTTGGCTACAGAC
* * *
61237 TGGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGAC
1 TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAGTATCAGTTGGCTACAGAC
* * * * *
61297 TAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCATTCAAGTATCAGTTGGCTACGGAC
1 TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAGTATCAGTTGGCTACAGAC
* * * * * ** **
61357 TGGCCTACTTC-AGTGTCGACCATAGATTGGTCTCTTCCAAGCGTCAGTAAGCTACAGAC
1 TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAGTATCAGTTGGCTACAGAC
* *
61416 TAGCCTACTTCAAGCATCGACCAC
1 TAGCCTACTTCAAGTATTGACCAC
61440 GGACTGGTTT
Statistics
Matches: 172, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
59 47 0.27
60 125 0.73
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (60 bp):
TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAGTATCAGTTGGCTACAGAC
Found at i:61281 original size:28 final size:28
Alignment explanation
Indices: 61185--61282 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
61175 AATAGCCTAC
61185 TTCAAGTATTGACCACGGATTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
* * *
61213 TTCAAGTATCAGTTGGCCACGGACTGGCCTAC-
1 TTCAAG--T-A-TTGACCACGGATTGGTCT-CT
*
61245 TTCAAGTATTGACCACAGATTGGTCTCT
1 TTCAAGTATTGACCACGGATTGGTCTCT
*
61273 TTCAGGTATT
1 TTCAAGTATT
61283 AGTTGGCTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
27 1 0.02
28 29 0.52
29 1 0.02
30 2 0.04
31 1 0.02
32 21 0.38
33 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (28 bp):
TTCAAGTATTGACCACGGATTGGTCTCT
Found at i:61292 original size:143 final size:143
Alignment explanation
Indices: 61034--61317 Score: 514
Period size: 143 Copynumber: 2.0 Consensus size: 143
61024 GGCTACAGAC
*
61034 TAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAATATCAGTTGGCCACGGACTGGCC
1 TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAATATCAGTTGGCCACGGACTGGCC
* *
61099 TACTTAAAGTGTTGACCACGGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGACTAGCCTACTT
66 TACTTAAAGTATTGACCACAGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGACTAGCCTACTT
61164 CAAGTGTTGACAA
131 CAAGTGTTGACAA
* *
61177 TAGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCC
1 TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAATATCAGTTGGCCACGGACTGGCC
*
61242 TACTTCAAGTATTGACCACAGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGACTAGCCTACTT
66 TACTTAAAGTATTGACCACAGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGACTAGCCTACTT
61307 CAAGTGTTGAC
131 CAAGTGTTGAC
61318 CACGGGTTGG
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 135 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (143 bp):
TAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAATATCAGTTGGCCACGGACTGGCC
TACTTAAAGTATTGACCACAGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGACTAGCCTACTT
CAAGTGTTGACAA
Found at i:61365 original size:203 final size:202
Alignment explanation
Indices: 61015--61381 Score: 554
Period size: 203 Copynumber: 1.8 Consensus size: 202
61005 GCGTCCCAAG
* *
61015 GTATCAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAATATC
1 GTATCAGTTGGCCACAGACTAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAATATC
* * * * *
61080 AGTTGGCCACGGACTGGCCTACTTAAAGTGTTGACCACGGATTGGTCTCTTTCAGGTATTAGTTG
66 AGTTGGCCACAGACTAGCCTACTTAAAGTGTTGACCACGGATTGGTCTCATTCAAGTATCAGTTG
*
61145 GCTACAGACTAGCCTACTTCAAGTGTTGACAATAGCCTACTTCAAGTATTGACCACGGATTGGTC
131 GCTACAGACTAGCCTACTTC-AGTGTCGACAATAGCCTACTTCAAGTATTGACCACGGATTGGTC
61210 TCTTTCAA
195 TCTTTCAA
* * ** *
61218 GTATCAGTTGGCCACGGACTGGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAGGTATT
1 GTATCAGTTGGCCACAGACTAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAATATC
* * *
61283 AGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCATTCAAGTATCAGTTG
66 AGTTGGCCACAGACTAGCCTACTTAAAGTGTTGACCACGGATTGGTCTCATTCAAGTATCAGTTG
* * *
61348 GCTACGGACTGGCCTACTTCAGTGTCGACCATAG
131 GCTACAGACTAGCCTACTTCAGTGTCGACAATAG
61382 ATTGGTCTCT
Statistics
Matches: 145, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
202 12 0.08
203 133 0.92
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (202 bp):
GTATCAGTTGGCCACAGACTAGCCTACTTCAAGTATTGACCACAGATTGGTCTCTTTCAAATATC
AGTTGGCCACAGACTAGCCTACTTAAAGTGTTGACCACGGATTGGTCTCATTCAAGTATCAGTTG
GCTACAGACTAGCCTACTTCAGTGTCGACAATAGCCTACTTCAAGTATTGACCACGGATTGGTCT
CTTTCAA
Found at i:61457 original size:119 final size:120
Alignment explanation
Indices: 61177--61447 Score: 382
Period size: 120 Copynumber: 2.3 Consensus size: 120
61167 GTGTTGACAA
*
61177 TAGCCTACTTCAAGTATTGACCACGGATTGGTCTCTTTCAAGTATCAGTTGGCCACGGACTGGCC
1 TAGCCTACTTCAAGTATTGACCACGGATTGGTCTCATTCAAGTATCAGTTGGCCACGGACTGGCC
* * * * * **
61242 TACTTCAAGTATTGACCACAGATTGGTCTCTTTCAGGTATTAGTTGGCTACAGAC
66 TACTTCAAGTATCGACCACAGATTGGTCTCTTCCAAGCATCAGTAAGCTACAGAC
* * *
61297 TAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCATTCAAGTATCAGTTGGCTACGGACTGGCC
1 TAGCCTACTTCAAGTATTGACCACGGATTGGTCTCATTCAAGTATCAGTTGGCCACGGACTGGCC
* * *
61362 TACTTC-AGTGTCGACCATAGATTGGTCTCTTCCAAGCGTCAGTAAGCTACAGAC
66 TACTTCAAGTATCGACCACAGATTGGTCTCTTCCAAGCATCAGTAAGCTACAGAC
* * *
61416 TAGCCTACTTCAAGCATCGACCACGGACTGGT
1 TAGCCTACTTCAAGTATTGACCACGGATTGGT
61448 TTTCTTCAAG
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
119 65 0.49
120 67 0.51
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (120 bp):
TAGCCTACTTCAAGTATTGACCACGGATTGGTCTCATTCAAGTATCAGTTGGCCACGGACTGGCC
TACTTCAAGTATCGACCACAGATTGGTCTCTTCCAAGCATCAGTAAGCTACAGAC
Found at i:61474 original size:27 final size:29
Alignment explanation
Indices: 61423--61480 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
61413 GACTAGCCTA
*
61423 CTTCAAGCATCGACCACGGACTGGT-TTT
1 CTTCAAGAATCGACCACGGACTGGTCTTT
* *
61451 CTTCAAGAAT-GACCATGGATTGGTCTTT
1 CTTCAAGAATCGACCACGGACTGGTCTTT
61479 CT
1 CT
61481 CTATGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (29 bp):
CTTCAAGAATCGACCACGGACTGGTCTTT
Done.