Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000946.1 Hibiscus syriacus cultivar Beakdansim tig00001893_pilon, 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: 47840
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:888 original size:23 final size:23
Alignment explanation
Indices: 862--907 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
852 CACCACAGCT
* * *
862 CGTATAATTGCACTGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
*
885 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
908 TATAATGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:1412 original size:149 final size:149
Alignment explanation
Indices: 885--1483 Score: 1159
Period size: 149 Copynumber: 4.0 Consensus size: 149
875 TGAAGTGCCA
* *
885 CGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
950 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1015 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1034 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1099 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTT--CACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1162 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1181 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1246 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1311 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1330 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1395 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCC-AAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1459 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1478 CGTAGA
1 CGTAGA
1484 CCCTCGACTC
Statistics
Matches: 446, Mismatches: 2, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
147 147 0.33
148 34 0.08
149 265 0.59
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:1419 original size:296 final size:296
Alignment explanation
Indices: 885--1483 Score: 1155
Period size: 296 Copynumber: 2.0 Consensus size: 296
875 TGAAGTGCCA
*
885 CGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
950 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1015 CATATGTCCCAAAGAACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCA
131 CATATGTCCCAAAGAACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCA
1080 CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTT-CA
196 CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTACA
1144 CATGTTCCAAAGAATATACATATGTCCCAAAGAACCG
261 CATGTTCC-AAGAATATACATATGTCCCAAAGAACCG
*
1181 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1246 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1311 CATATGTCCCAAAGAACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCA
131 CATATGTCCCAAAGAACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCA
1376 CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCAC
196 CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTT-AC
1441 ACATGTTCCAAGAATATACATATGTCCCAAAGAACCG
260 ACATGTTCCAAGAATATACATATGTCCCAAAGAACCG
1478 CGTAGA
1 CGTAGA
1484 CCCTCGACTC
Statistics
Matches: 299, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
296 255 0.85
297 34 0.11
298 10 0.03
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (296 bp):
CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCA
CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTACA
CATGTTCCAAGAATATACATATGTCCCAAAGAACCG
Found at i:2401 original size:18 final size:18
Alignment explanation
Indices: 2380--2414 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2370 TCCCATCTAG
2380 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2398 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2415 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3022 original size:21 final size:21
Alignment explanation
Indices: 2998--3042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2988 TCTTGTTCGT
* *
2998 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3019 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3040 TTG
1 TTG
3043 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3983 original size:20 final size:20
Alignment explanation
Indices: 3958--3995 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3948 TTTATTATTA
3958 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
3978 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
3996 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:4038 original size:17 final size:16
Alignment explanation
Indices: 4006--4039 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3996 TTTACTCATT
*
4006 TATTTATCTATTTTTA
1 TATTTATCTATATTTA
4022 TATTTATCCTATATTTA
1 TATTTAT-CTATATTTA
4039 T
1 T
4040 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATCTATATTTA
Found at i:5327 original size:5 final size:5
Alignment explanation
Indices: 5317--5345 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5307 TTCATCTTTC
5317 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5346 CATCACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:6747 original size:7 final size:7
Alignment explanation
Indices: 6728--6766 Score: 51
Period size: 8 Copynumber: 5.1 Consensus size: 7
6718 GAACATTTCA
6728 TGCATTCT
1 TGCATT-T
6736 TGCATTT
1 TGCATTT
6743 TGCATTTT
1 TGCA-TTT
6751 TGCCATTT
1 TG-CATTT
6759 TGCATTT
1 TGCATTT
6766 T
1 T
6767 CATCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 11 0.38
8 16 0.55
9 2 0.07
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:6759 original size:16 final size:15
Alignment explanation
Indices: 6728--6766 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
6718 GAACATTTCA
*
6728 TGCATTCTTGCATTT
1 TGCATTTTTGCATTT
6743 TGCATTTTTGCCATTT
1 TGCATTTTTG-CATTT
6759 TGCATTTT
1 TGCATTTT
6767 CATCTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.56
Consensus pattern (15 bp):
TGCATTTTTGCATTT
Found at i:7961 original size:9 final size:9
Alignment explanation
Indices: 7949--7987 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
7939 TAAAAAGGGC
7949 AAAAAGAAA
1 AAAAAGAAA
*
7958 AAAAAGCAA
1 AAAAAGAAA
*
7967 AAAAAGAAC
1 AAAAAGAAA
7976 AAAAAGAAA
1 AAAAAGAAA
7985 AAA
1 AAA
7988 GAAAAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:7961 original size:18 final size:17
Alignment explanation
Indices: 7935--7993 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
7925 ATATTTAATC
* *
7935 AGAATAAAAAGGGCAAAA
1 AGAA-AAAAAAGGAAAAA
*
7953 AGAAAAAAAAGCAAAAAA
1 AGAAAAAAAAG-GAAAAA
*
7971 AGAACAAAAA-GAAAAA
1 AGAAAAAAAAGGAAAAA
7987 AGAAAAA
1 AGAAAAA
7994 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.32
17 6 0.18
18 17 0.50
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAGGAAAAA
Found at i:7966 original size:16 final size:16
Alignment explanation
Indices: 7947--7993 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
7937 AATAAAAAGG
7947 GCAAAAAGAAAAAAAA
1 GCAAAAAGAAAAAAAA
*
7963 GCAAAAAAAGAACAAAAA
1 GC--AAAAAGAAAAAAAA
*
7981 GAAAAAAGAAAAA
1 GCAAAAAGAAAAA
7994 GGGACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (16 bp):
GCAAAAAGAAAAAAAA
Found at i:8619 original size:22 final size:22
Alignment explanation
Indices: 8591--8634 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
8581 AGCTACCCCA
8591 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
8613 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
8635 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:9653 original size:36 final size:36
Alignment explanation
Indices: 9606--9868 Score: 272
Period size: 36 Copynumber: 7.4 Consensus size: 36
9596 ATTGAAAACA
* *
9606 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
9642 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
9679 TTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
9715 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * *
9744 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
9780 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
9817 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
9853 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
9869 ATCTTTGAAT
Statistics
Matches: 188, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 2 0.01
35 1 0.01
36 99 0.53
37 65 0.35
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:9754 original size:102 final size:102
Alignment explanation
Indices: 9648--9832 Score: 300
Period size: 102 Copynumber: 1.8 Consensus size: 102
9638 ATAGTTTCCC
* *
9648 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTT-GAAATAAATTTTGTCTCTCTTGAGA
1 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTCTTGGAAATAAATTTTGTCTCTCTTGAGA
9712 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
* * *
9750 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGGAAATAAATTTTGTCTCTCTTGAGAC
*
9815 AGTTTCTCTTGAAACAAA
66 AGTTTCCCTTGAAACAAA
9833 TTTCGTCTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
101 28 0.37
102 48 0.63
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (102 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
Found at i:9806 original size:138 final size:138
Alignment explanation
Indices: 9540--9931 Score: 509
Period size: 138 Copynumber: 2.8 Consensus size: 138
9530 ACTCATGATT
* * * * *
9540 GTTTTTCTTAAAACAAGA-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACA-TTGAAA
1 GTTTCTCTTGAAACAA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATATTTGAAT
* * * *
9603 ACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
64 ATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTC
9668 TCTTGAGACA
129 TCTTGAGACA
*
9678 GTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
* * * ** * * *
9743 GTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
66 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
9808 TTGAGACA
131 TTGAGACA
* * * *
9816 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
* * * * *
9881 ATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
66 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACA
9932 CAAAATCTTC
Statistics
Matches: 219, Mismatches: 33, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
137 5 0.02
138 214 0.98
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (138 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
TTGAGACA
Found at i:9930 original size:65 final size:65
Alignment explanation
Indices: 9826--10000 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
9816 GTTTCTCTTG
* ** * **
9826 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
9891 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
9956 TA
64 TA
* * *
9958 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
10001 CATATATCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:10765 original size:105 final size:105
Alignment explanation
Indices: 10604--11053 Score: 703
Period size: 105 Copynumber: 4.3 Consensus size: 105
10594 GTCATCCGTG
* * * *
10604 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
10669 GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
10712 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
10777 ACCGCTGCTTGTCAATAACAACTTCCCAATCGCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
10817 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
10882 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
10922 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
10987 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
11022 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
11054 TGAACAATGC
Statistics
Matches: 323, Mismatches: 19, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
100 37 0.11
101 2 0.01
102 1 0.00
103 2 0.01
104 2 0.01
105 254 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:14391 original size:12 final size:12
Alignment explanation
Indices: 14354--14392 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
14344 ATCTGATACT
14354 TGACATGGATTC
1 TGACATGGATTC
*
14366 TGATAT-GATATC
1 TGACATGGAT-TC
14378 TGACATGGATTC
1 TGACATGGATTC
14390 TGA
1 TGA
14393 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:14470 original size:24 final size:24
Alignment explanation
Indices: 14339--14453 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
14329 TCGATTTGAT
*
14339 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
14363 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
14387 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
14411 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
14435 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
14454 GTGAATTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:15933 original size:25 final size:25
Alignment explanation
Indices: 15885--15933 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
15875 TTTAAATTAT
*
15885 GTTAAAATATTTTTTAATTGTAATG
1 GTTAAAATATTTTTAAATTGTAATG
*
15910 GTTATAATATTTTGTAAATT-TAAT
1 GTTAAAATATTTT-TAAATTGTAAT
15934 AATTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (25 bp):
GTTAAAATATTTTTAAATTGTAATG
Found at i:26487 original size:137 final size:137
Alignment explanation
Indices: 26238--26511 Score: 503
Period size: 137 Copynumber: 2.0 Consensus size: 137
26228 TATCGTCACT
*
26238 AGTAACTAACCATCGATCGTTATTTGCGACAACGTTGATATCAAAATATTCACATTCTACTCCTC
1 AGTAACTAACCATCGATCGTTATTGGCGACAACGTTGATATCAAAATATTCACATTCTACTCCTC
26303 TTTCTTTTCATTAGATTAGTAGTTCACGAAATCATTCAAAATCAATGAAAATCCATTTAGAGGTT
66 TTTCTTTTCATTAGATTAGTAGTTCACGAAATCATTCAAAATCAATGAAAATCCATTTAGAGGTT
26368 CGACATA
131 CGACATA
*
26375 AGTAACTAACCATCGATCGTTATTGGCGACAACGTTGATATCAAAATATTCACATTTTACTCCTC
1 AGTAACTAACCATCGATCGTTATTGGCGACAACGTTGATATCAAAATATTCACATTCTACTCCTC
* * *
26440 TTTCTTTTCATTAGATTGGTAGTTCACGAAATCATTCAAAATTAATGAAAATTCATTTAGAGGTT
66 TTTCTTTTCATTAGATTAGTAGTTCACGAAATCATTCAAAATCAATGAAAATCCATTTAGAGGTT
26505 CGACATA
131 CGACATA
26512 CTAATACTCC
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (137 bp):
AGTAACTAACCATCGATCGTTATTGGCGACAACGTTGATATCAAAATATTCACATTCTACTCCTC
TTTCTTTTCATTAGATTAGTAGTTCACGAAATCATTCAAAATCAATGAAAATCCATTTAGAGGTT
CGACATA
Found at i:27308 original size:37 final size:32
Alignment explanation
Indices: 27267--27382 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 32
27257 TAAATATCTA
*
27267 TAATATTAAAAAATGAATATTTAATTTATTTAAAAAT
1 TAATATT--AAAATGAATA--TAATATA-TTAAAAAT
*
27304 TAATATTAAAATTAATATAATATATTAAAAAT
1 TAATATTAAAATGAATATAATATATTAAAAAT
27336 TAATATT----T-AAT-T--TAT-TTAAAAAT
1 TAATATTAAAATGAATATAATATATTAAAAAT
*
27359 TAATATTAAAATCAATATAATATA
1 TAATATTAAAATGAATATAATATA
27383 AAATTAAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
23 15 0.22
24 3 0.04
26 1 0.01
27 4 0.06
28 4 0.06
29 1 0.01
31 3 0.04
32 15 0.22
33 6 0.09
35 9 0.13
37 7 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (32 bp):
TAATATTAAAATGAATATAATATATTAAAAAT
Found at i:27314 original size:12 final size:12
Alignment explanation
Indices: 27299--27376 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
27289 AATTTATTTA
27299 AAAATTAATATT
1 AAAATTAATATT
27311 AAAATTAATA-T
1 AAAATTAATATT
27322 --AA-T-ATATT
1 AAAATTAATATT
27330 AAAAATTAATATT
1 -AAAATTAATATT
* *
27343 -TAATTTAT-TT
1 AAAATTAATATT
27353 AAAAATTAATATT
1 -AAAATTAATATT
*
27366 AAAATCAATAT
1 AAAATTAATAT
27377 AATATAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 2 0.04
10 2 0.04
11 9 0.17
12 27 0.52
13 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:27326 original size:17 final size:17
Alignment explanation
Indices: 27304--27395 Score: 66
Period size: 17 Copynumber: 5.2 Consensus size: 17
27294 ATTTAAAAAT
27304 TAATATTAAAATTAATA
1 TAATATTAAAATTAATA
27321 TAATATATTAAAAATTAATA
1 T-A-ATATT-AAAATTAATA
*
27341 TTTAATTTATTTAAA--AAT-
1 --TAA--TATTAAAATTAATA
*
27359 TAATATTAAAATCAATA
1 TAATATTAAAATTAATA
27376 TAATA-TAAAATTAAATA
1 TAATATTAAAATT-AATA
27393 TAA
1 TAA
27396 AACCTCTTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 22
0.71 0.03 0.26
Matches are distributed among these distances:
14 7 0.11
16 12 0.20
17 13 0.21
18 1 0.02
19 8 0.13
20 11 0.18
21 4 0.07
22 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTAAAATTAATA
Found at i:27337 original size:32 final size:32
Alignment explanation
Indices: 27296--27382 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 32
27286 TTTAATTTAT
27296 TTAAAAATTAATATTAAAATTAATATAATATA
1 TTAAAAATTAATATTAAAATTAATATAATATA
27328 TTAAAAATTAATA-T----TTAAT-T--TAT-
1 TTAAAAATTAATATTAAAATTAATATAATATA
*
27351 TTAAAAATTAATATTAAAATCAATATAATATA
1 TTAAAAATTAATATTAAAATTAATATAATATA
27383 AAATTAAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 18
0.70 0.02 0.28
Matches are distributed among these distances:
23 13 0.29
24 4 0.09
26 1 0.02
27 5 0.11
28 4 0.09
29 1 0.02
31 4 0.09
32 13 0.29
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
TTAAAAATTAATATTAAAATTAATATAATATA
Found at i:27345 original size:55 final size:55
Alignment explanation
Indices: 27265--27382 Score: 202
Period size: 55 Copynumber: 2.2 Consensus size: 55
27255 ATTAAATATC
*
27265 TATAATAT-TAAAAAATGAATATTTAATTTATTTAAAAATTAATATTAAAATTAA
1 TATAATATATAAAAAATGAATATTTAATTTATTTAAAAATTAATATTAAAATCAA
* *
27319 TATAATATATTAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATCAA
1 TATAATATATAAAAAATGAATATTTAATTTATTTAAAAATTAATATTAAAATCAA
27374 TATAATATA
1 TATAATATA
27383 AAATTAAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
54 8 0.13
55 52 0.87
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (55 bp):
TATAATATATAAAAAATGAATATTTAATTTATTTAAAAATTAATATTAAAATCAA
Found at i:28730 original size:24 final size:24
Alignment explanation
Indices: 28703--28749 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28693 AATATATATA
*
28703 TATATATACTTTTTAATAAAATTG
1 TATATATAATTTTTAATAAAATTG
*
28727 TATATATAATTTTTTATAAAATT
1 TATATATAATTTTTAATAAAATT
28750 TAAAAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TATATATAATTTTTAATAAAATTG
Found at i:30565 original size:21 final size:21
Alignment explanation
Indices: 30539--30580 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30529 CCAGAATGGG
*
30539 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
30560 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
30581 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Done.