Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004926.1 Hibiscus syriacus cultivar Beakdansim tig00011090_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: 51246
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6563 original size:22 final size:22
Alignment explanation
Indices: 6522--6568 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
6512 TGTTTCTTCT
*
6522 TTTTGAGTGCTTGATTTTTTTC
1 TTTTGAGTGCTTGATCTTTTTC
6544 TTTTGAGTGCTTGCA-CTTTTTC
1 TTTTGAGTGCTTG-ATCTTTTTC
6566 TTT
1 TTT
6569 CCTGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTTGAGTGCTTGATCTTTTTC
Found at i:8758 original size:35 final size:35
Alignment explanation
Indices: 8717--8830 Score: 158
Period size: 35 Copynumber: 3.2 Consensus size: 35
8707 TGGTAAGGGA
* *
8717 ATGGTGATTATATAGGCTTGAAATGGTGATAGAAG
1 ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
* * *
8752 ATGGTGATGATATAGGCGTGTAATGGTGATGGAAA
1 ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
8787 ATGGTGATGT-TATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGAT-TATATAGGCGTG-AAATGGTGATGGAAG
8823 ATGGTGAT
1 ATGGTGAT
8831 GAACAGATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 48 0.70
36 21 0.30
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.30
Consensus pattern (35 bp):
ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
Found at i:8791 original size:13 final size:13
Alignment explanation
Indices: 8773--8831 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
8763 ATAGGCGTGT
8773 AATGGTGATGGAA
1 AATGGTGATGGAA
**
8786 AATGGTGATGTTA
1 AATGGTGATGGAA
* *
8799 TA-GGCG-T-GAA
1 AATGGTGATGGAA
8809 AATGGTGATGGAA
1 AATGGTGATGGAA
*
8822 GATGGTGATG
1 AATGGTGATG
8832 AACAGATAGT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 24 0.71
ACGTcount: A:0.32, C:0.02, G:0.39, T:0.27
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:12607 original size:15 final size:16
Alignment explanation
Indices: 12587--12644 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
12577 AGGATATGGT
12587 AATGAAATAAGAAA-A
1 AATGAAATAAGAAAGA
* *
12602 AATGAAAGAATAAAGA
1 AATGAAATAAGAAAGA
*
12618 AATGAAAT-AGTAAGA
1 AATGAAATAAGAAAGA
12633 AAGTGAAGATAA
1 AA-TGAA-ATAA
12645 CTTACAACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 19 0.56
16 12 0.35
17 2 0.06
18 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.16
Consensus pattern (16 bp):
AATGAAATAAGAAAGA
Found at i:12847 original size:5 final size:5
Alignment explanation
Indices: 12837--12862 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12827 GATGTATGAG
12837 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
12863 TCTTGTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:13255 original size:35 final size:35
Alignment explanation
Indices: 13216--13320 Score: 129
Period size: 35 Copynumber: 3.0 Consensus size: 35
13206 AATAGTTATT
* * **
13216 ATATAAGCGTGAAATGGGGATACAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
13251 ATATAGGCGTGCAATGGTGATGGAAAATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
13286 TTATAGGTGTGAAAATGGTGATGGAAGATGGTGAT
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGTGAT
13321 CAATAGATAG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
35 38 0.64
36 21 0.36
ACGTcount: A:0.33, C:0.04, G:0.36, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:13281 original size:13 final size:13
Alignment explanation
Indices: 13263--13320 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
13253 ATAGGCGTGC
13263 AATGGTGATGGAA
1 AATGGTGATGGAA
**
13276 AATGGTGATGTTA
1 AATGGTGATGGAA
*
13289 TA-GGTG-T-GAA
1 AATGGTGATGGAA
13299 AATGGTGATGGAA
1 AATGGTGATGGAA
*
13312 GATGGTGAT
1 AATGGTGAT
13321 CAATAGATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 23 0.66
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:25880 original size:7 final size:8
Alignment explanation
Indices: 25853--25920 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
25843 TGAACTTATC
25853 TTTTTCTT
1 TTTTTCTT
25861 TCCTTTTCTT
1 T--TTTTCTT
25871 TTTTTCTT
1 TTTTTCTT
25879 TTTTTCTGAT
1 TTTTTCT--T
25889 TTTTCTCTTCT
1 TTTT-TC-T-T
25900 TTTTGTCTT
1 TTTT-TCTT
25909 TTCTTTCTT
1 TT-TTTCTT
25918 TTT
1 TTT
25921 GCACTGTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
8 16 0.31
9 9 0.18
10 16 0.31
11 9 0.18
12 1 0.02
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTTTCTT
Found at i:25921 original size:17 final size:17
Alignment explanation
Indices: 25853--25919 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 17
25843 TGAACTTATC
*
25853 TTTTTCTTTCCTTTTCTT
1 TTTTTCTTT-CTTTTCTG
25871 TTTTTCTTT-TTTTCTG
1 TTTTTCTTTCTTTTCTG
25887 ATTTTTCTCTTCTTTT-TG
1 -TTTTTCT-TTCTTTTCTG
25905 TCTTTTCTTTCTTTT
1 T-TTTTCTTTCTTTT
25920 TGCACTGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
16 6 0.14
17 15 0.34
18 19 0.43
19 4 0.09
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTCTTTTCTG
Found at i:31784 original size:36 final size:36
Alignment explanation
Indices: 31737--31840 Score: 140
Period size: 35 Copynumber: 2.9 Consensus size: 36
31727 CTACCTAAAC
31737 ATCACCATCTTCCATCACCATTTTCACGCCTATAAT-
1 ATCACCATCTTCCATCACCA-TTTCACGCCTATAATG
* *
31773 ATCACCATCTTCCATTACCATTGCACGCCTAT-ATG
1 ATCACCATCTTCCATCACCATTTCACGCCTATAATG
* * *
31808 ATTACCATCTTCTAGCACCATTTCACGCCTATA
1 ATCACCATCTTCCATCACCATTTCACGCCTATA
31841 CAATTGCCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 2 0.03
35 38 0.64
36 19 0.32
ACGTcount: A:0.27, C:0.35, G:0.06, T:0.33
Consensus pattern (36 bp):
ATCACCATCTTCCATCACCATTTCACGCCTATAATG
Found at i:37316 original size:35 final size:35
Alignment explanation
Indices: 37275--37388 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 35
37265 TGGTAAGGGA
** *
37275 ATGGTGATTATATATAAGTGAAATGGTGATAGAAG
1 ATGGTGATTATATAGGAGTGAAATGGTGATGGAAG
* * * *
37310 ATGGTGATGATATAGGCGTGCAATGGTGATGGAAA
1 ATGGTGATTATATAGGAGTGAAATGGTGATGGAAG
*
37345 ATGGTGATGT-TATAGGTGTGAAAATGGTGATGGAAG
1 ATGGTGAT-TATATAGGAGTG-AAATGGTGATGGAAG
37381 ATGGTGAT
1 ATGGTGAT
37389 GAATAGATAG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 45 0.68
36 21 0.32
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (35 bp):
ATGGTGATTATATAGGAGTGAAATGGTGATGGAAG
Found at i:37349 original size:13 final size:13
Alignment explanation
Indices: 37331--37389 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
37321 ATAGGCGTGC
37331 AATGGTGATGGAA
1 AATGGTGATGGAA
**
37344 AATGGTGATGTTA
1 AATGGTGATGGAA
*
37357 TA-GGTG-T-GAA
1 AATGGTGATGGAA
37367 AATGGTGATGGAA
1 AATGGTGATGGAA
*
37380 GATGGTGATG
1 AATGGTGATG
37390 AATAGATAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 24 0.67
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:43516 original size:24 final size:21
Alignment explanation
Indices: 43489--43534 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
43479 AGAATTGTTG
43489 TTGAGTGCTTACAAATTTCTTCTT
1 TTGAGTG-TTAC-AATTT-TTCTT
*
43513 TTGAGTGTTTCAATTTTTCTT
1 TTGAGTGTTACAATTTTTCTT
43534 T
1 T
43535 GCTGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 3 0.14
24 7 0.33
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (21 bp):
TTGAGTGTTACAATTTTTCTT
Found at i:46317 original size:22 final size:22
Alignment explanation
Indices: 46291--46332 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
46281 TATTTATAGT
*
46291 TATGATGATGATATTATGAATG
1 TATGAAGATGATATTATGAATG
* *
46313 TATGAAGTTGTTATTATGAA
1 TATGAAGATGATATTATGAA
46333 CCACATATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (22 bp):
TATGAAGATGATATTATGAATG
Done.