Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004303.1 Hibiscus syriacus cultivar Beakdansim tig00009436_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: 74333
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:8045 original size:46 final size:46
Alignment explanation
Indices: 8005--8115 Score: 204
Period size: 46 Copynumber: 2.4 Consensus size: 46
7995 ATTTTAAATT
*
8005 ATTAGTTTGATAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
1 ATTAGTTTGTTAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
*
8051 ATTAGTTTGTTAGTTTAGGGTTTAAGGTAAAACAAAATTTTAGTTA
1 ATTAGTTTGTTAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
8097 ATTAGTTTGTTAGTTTAAG
1 ATTAGTTTGTTAGTTTAAG
8116 TTATATTATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (46 bp):
ATTAGTTTGTTAGTTTAAGGTTTAAGGTAAAACAAAATTTTAGTTA
Found at i:8275 original size:44 final size:46
Alignment explanation
Indices: 8180--8276 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 46
8170 AGTTTGTTTG
* * **
8180 ATAGTTATATATTAAAAAAATAATTAATTAGTTTGTTTGTTAGTCG
1 ATAGTTATATAATAAAAAAATAATTAATTAGTTTGTTAGTTAGTAA
* *
8226 TTAGTTATA-AAT-AAAAAATATTTAATTAGTTTG-TAGTTAGTTAA
1 ATAGTTATATAATAAAAAAATAATTAATTAGTTTGTTAGTTAG-TAA
8270 ATAGTTA
1 ATAGTTA
8277 AGTTATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 6 0.14
44 27 0.63
45 2 0.05
46 8 0.19
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.45
Consensus pattern (46 bp):
ATAGTTATATAATAAAAAAATAATTAATTAGTTTGTTAGTTAGTAA
Found at i:11672 original size:28 final size:30
Alignment explanation
Indices: 11632--11694 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
11622 ATTTTTTATA
11632 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
11662 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
11690 TAATA
1 TAATA
11695 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:11701 original size:28 final size:28
Alignment explanation
Indices: 11636--11701 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
11626 TTTATATAAT
11636 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
11664 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
11692 ATAATTTATA
1 ATAATATATA
11702 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:11704 original size:21 final size:21
Alignment explanation
Indices: 11671--11719 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
11661 CTAATATAAT
11671 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
11692 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
11713 ATTAACT
1 A-TAACT
11720 AAAATTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:14776 original size:18 final size:20
Alignment explanation
Indices: 14753--14793 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
14743 CACTTGTCAA
14753 ATTATTAGTTTT-AAA-AAT
1 ATTATTAGTTTTGAAAGAAT
*
14771 ATTATTTGTTTTGAAAGAAT
1 ATTATTAGTTTTGAAAGAAT
14791 ATT
1 ATT
14794 CACCCTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 3 0.15
20 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTATTAGTTTTGAAAGAAT
Found at i:15721 original size:18 final size:18
Alignment explanation
Indices: 15683--15721 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
15673 TTTCGAGATA
* * *
15683 AAACACCCAAATTCGATG
1 AAACACCCAAACTCAACG
15701 AAACACCCAAACTCAACG
1 AAACACCCAAACTCAACG
15719 AAA
1 AAA
15722 AACAATTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.31, G:0.08, T:0.10
Consensus pattern (18 bp):
AAACACCCAAACTCAACG
Found at i:22752 original size:60 final size:59
Alignment explanation
Indices: 22617--22791 Score: 165
Period size: 60 Copynumber: 2.9 Consensus size: 59
22607 TCAAACTATA
* * * * * * *
22617 ACTCTCATTCTAACTTAGCCCCTAAACATTTGAACATTTCAATGTCATCCCTAAATTATG
1 ACTCTCATTCCAAATTAGTCCC-AAACTTTTGAACATTTCAATTTCATTCCAAAATTATG
** ** ** *
22677 ACTCTCATTTTAAATTAGTCTTTACGCTTTTGAACATTTTAATTTCATTCCAAAATTATG
1 ACTCTCATTCCAAATTAGTC-CCAAACTTTTGAACATTTCAATTTCATTCCAAAATTATG
*
22737 AC-CTTCATTCCAAATTGGTCCCAAACTTTTGAACATTTCAATTTC-TTCACAAAAT
1 ACTC-TCATTCCAAATTAGTCCCAAACTTTTGAACATTTCAATTTCATTC-CAAAAT
22792 ATAGGTATAT
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
58 3 0.03
59 27 0.29
60 62 0.67
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.39
Consensus pattern (59 bp):
ACTCTCATTCCAAATTAGTCCCAAACTTTTGAACATTTCAATTTCATTCCAAAATTATG
Found at i:24209 original size:4 final size:4
Alignment explanation
Indices: 24200--24261 Score: 94
Period size: 4 Copynumber: 16.2 Consensus size: 4
24190 TAACATTTAC
*
24200 TATT TATT TATT TATT TATT TATT TATT TATT T-TC T-TT TA-T TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
24245 TATT TATT TATT TATT T
1 TATT TATT TATT TATT T
24262 TTGTTTTAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 7 0.13
4 47 0.87
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:24959 original size:13 final size:13
Alignment explanation
Indices: 24941--24965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24931 TTTTAGGTGA
24941 AAATTGTAAGTTT
1 AAATTGTAAGTTT
24954 AAATTGTAAGTT
1 AAATTGTAAGTT
24966 AATTTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
AAATTGTAAGTTT
Found at i:29241 original size:23 final size:23
Alignment explanation
Indices: 29201--29244 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29191 CTCGAGACTC
* * *
29201 GAGCTCTATTGAAGCTCGATTTT
1 GAGCTCGATTCAAACTCGATTTT
29224 GAGCTCGATTCAAACTCGATT
1 GAGCTCGATTCAAACTCGATT
29245 CAAGCTCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
GAGCTCGATTCAAACTCGATTTT
Found at i:29258 original size:17 final size:17
Alignment explanation
Indices: 29236--29274 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
29226 GCTCGATTCA
29236 AACTCGATTCAAGCTCG
1 AACTCGATTCAAGCTCG
29253 AACTCGATTCAAGCTCG
1 AACTCGATTCAAGCTCG
29270 AACTC
1 AACTC
29275 AAACTCGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (17 bp):
AACTCGATTCAAGCTCG
Found at i:29270 original size:11 final size:11
Alignment explanation
Indices: 29202--29253 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
29192 TCGAGACTCG
* *
29202 AGCTCTATTGA
1 AGCTCGATTCA
**
29213 AGCTCGATTTTG
1 AGCTCGA-TTCA
29225 AGCTCGATTCA
1 AGCTCGATTCA
*
29236 AACTCGATTCA
1 AGCTCGATTCA
29247 AGCTCGA
1 AGCTCGA
29254 ACTCGATTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:31778 original size:7 final size:7
Alignment explanation
Indices: 31766--31800 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
31756 CACATAATCA
31766 GGTTTAG
1 GGTTTAG
31773 GGTTTAG
1 GGTTTAG
31780 GGTTTAG
1 GGTTTAG
31787 GGTTTAG
1 GGTTTAG
31794 GGTTTAG
1 GGTTTAG
31801 TATTTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:31806 original size:14 final size:14
Alignment explanation
Indices: 31768--31839 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
31758 CATAATCAGG
*
31768 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGA
*
31782 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGA
** *
31796 TTTAGTATTTAAGA
1 TTTAGGGTTTAGGA
**
31810 TTTATAGTTTAGGA
1 TTTAGGGTTTAGGA
* *
31824 TTTAAGGTTTATGA
1 TTTAGGGTTTAGGA
31838 TT
1 TT
31840 CATTACAAAG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:31835 original size:21 final size:21
Alignment explanation
Indices: 31765--31834 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
31755 TCACATAATC
*
31765 AGGTTTAGGGTTTAGGGTTTA
1 AGGTTTAGGGTTTAGGATTTA
* *
31786 GGGTTTAGGGTTTAGTATTTA
1 AGGTTTAGGGTTTAGGATTTA
* **
31807 AGATTTATAGTTTAGGATTTA
1 AGGTTTAGGGTTTAGGATTTA
31828 AGGTTTA
1 AGGTTTA
31835 TGATTCATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (21 bp):
AGGTTTAGGGTTTAGGATTTA
Found at i:31927 original size:7 final size:7
Alignment explanation
Indices: 31915--31951 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
31905 AGGGTTAGAA
31915 TTTATGG
1 TTTATGG
*
31922 TTTATGT
1 TTTATGG
31929 TTTATGG
1 TTTATGG
31936 TTTATGG
1 TTTATGG
31943 TTTATGG
1 TTTATGG
31950 TT
1 TT
31952 AGGGTTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (7 bp):
TTTATGG
Found at i:31974 original size:7 final size:7
Alignment explanation
Indices: 31894--31978 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
31884 GCAAGTATAA
31894 TTTAGGG
1 TTTAGGG
31901 TTTAAGGG
1 TTT-AGGG
**
31909 -TTAGAA
1 TTTAGGG
*
31915 TTTATGG
1 TTTAGGG
* *
31922 TTTATGT
1 TTTAGGG
*
31929 TTTATGG
1 TTTAGGG
*
31936 TTTATGG
1 TTTAGGG
*
31943 TTTATGG
1 TTTAGGG
31950 -TTAGGG
1 TTTAGGG
31956 -TTAGGG
1 TTTAGGG
31962 -TTAGGG
1 TTTAGGG
31968 TTTAGGG
1 TTTAGGG
31975 TTTA
1 TTTA
31979 CGATTCATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
6 19 0.28
7 44 0.66
8 4 0.06
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:33495 original size:2 final size:2
Alignment explanation
Indices: 33488--33545 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
33478 ATTATAAACC
33488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33530 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
33546 GTTGTACTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35221 original size:22 final size:22
Alignment explanation
Indices: 35184--35248 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
35174 AGGCGATGAC
* **
35184 GTCAGCACCTTCTAGAAGTTCCA
1 GTCAGCA-TTTCTAGAAGCACCA
35207 GTCAGCATTTCTAGAAGCACCA
1 GTCAGCATTTCTAGAAGCACCA
*
35229 GTCAGCGTTTCTAGAAGCAC
1 GTCAGCATTTCTAGAAGCAC
35249 GAATGGATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
22 31 0.82
23 7 0.18
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (22 bp):
GTCAGCATTTCTAGAAGCACCA
Found at i:35455 original size:19 final size:19
Alignment explanation
Indices: 35352--35460 Score: 57
Period size: 19 Copynumber: 5.8 Consensus size: 19
35342 GGTATTTTAG
*
35352 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
35371 TTTAATTAAGTTTTAGATAT
1 TTTAATTAGGTTTTAG-TAT
* ** *
35391 TATT-TTTATATTTTA-TCT
1 T-TTAATTAGGTTTTAGTAT
* *
35409 TTGT-TTTAGGTATTT--TAG
1 TT-TAATTAGGT-TTTAGTAT
*
35427 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
35446 TTTAATTAGGATTTA
1 TTTAATTAGGTTTTA
35461 TGATATTATT
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
17 5 0.07
18 17 0.25
19 32 0.47
20 12 0.18
21 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:35536 original size:76 final size:75
Alignment explanation
Indices: 35328--35536 Score: 323
Period size: 75 Copynumber: 2.8 Consensus size: 75
35318 ACATTATTTT
* *
35328 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGATATTA
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGATATTA
* *
35393 TTTTTATATT
66 TTTTTAAATA
35403 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATGATATT
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA-GATATT
35468 A-TTTTAAATA
65 ATTTTTAAATA
* *
35478 TTATTTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTTAATTAGGATTTA
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGT-ATTTTAATTAGGATTTA
35537 AGATGTTTTA
Statistics
Matches: 125, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
74 5 0.04
75 97 0.78
76 23 0.18
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.58
Consensus pattern (75 bp):
TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGATATTA
TTTTTAAATA
Found at i:43934 original size:75 final size:75
Alignment explanation
Indices: 43806--44020 Score: 263
Period size: 75 Copynumber: 2.9 Consensus size: 75
43796 ATTTTAAACA
*
43806 TTATATTTTATCTTTGTTTTA-ATTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTT
1 TTATATTTTATCTTTGTTTTAGA-TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTT
*
43870 AGGATATTTTT
65 AGGATATTATT
* * * *
43881 TTATGTTTTATCTTTATTTTAGATATTTCAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
43946 TGATATTATT
66 GGATATTATT
* * * ** * * *
43956 TTAAATATTATTTTTGTTTTAGGCATTTTAGTTTAAATA-GTTTAAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTT-TAGTATTTTAATTAAGATTT
44020 A
65 A
44021 AGATGTTTTA
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
74 4 0.03
75 116 0.96
76 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GGATATTATT
Found at i:53063 original size:35 final size:35
Alignment explanation
Indices: 53017--53091 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
53007 CGTCACGAAC
*
53017 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
53052 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
53087 AGTAA
1 AGTAA
53092 TCTTCCTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:53202 original size:24 final size:23
Alignment explanation
Indices: 53174--53239 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 23
53164 ATTCAAGTCA
*
53174 AGTATCATATCAGAATCCATATC
1 AGTATCAGATCAGAATCCATATC
*
53197 ATGTATCAGATTAGAATCCATATC
1 A-GTATCAGATCAGAATCCATATC
*
53221 AATATCAGATCAGAATCCA
1 AGTATCAGATCAGAATCCA
53240 GGTCAGGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATATC
Found at i:54413 original size:18 final size:18
Alignment explanation
Indices: 54392--54427 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54382 CTTCCATCCG
*
54392 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
54410 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
54428 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:55659 original size:18 final size:18
Alignment explanation
Indices: 55636--55705 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
55626 AACAGTCAAC
55636 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
55654 GGTCAA----T-GGGTTG
1 GGTCAACGGGTCGGGTCG
*
55667 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
55685 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
55703 GGT
1 GGT
55706 TGTGACCGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
17 1 0.02
18 31 0.72
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:55675 original size:31 final size:31
Alignment explanation
Indices: 55640--55700 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
55630 GTCAACGGTC
* *
55640 AACGGGTCGGGTCGGGTCAATGGGTTGGGTA
1 AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
55671 AACGGGTCGGGTCGGGTCAACGGGTCGGGT
1 AACGGGTCGGGTCGGGTCAACGGGTCGGGT
55701 CGGGTTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.16, G:0.49, T:0.20
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
Found at i:56857 original size:22 final size:22
Alignment explanation
Indices: 56831--56876 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
56821 TAATTAGTTA
*
56831 ATTAATATTTATCGTTAAATAT
1 ATTAATATTGATCGTTAAATAT
*
56853 ATTAATATTGATTGTTAAATAT
1 ATTAATATTGATCGTTAAATAT
56875 AT
1 AT
56877 AGGTTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTAATATTGATCGTTAAATAT
Found at i:56961 original size:6 final size:6
Alignment explanation
Indices: 56936--57007 Score: 110
Period size: 6 Copynumber: 12.2 Consensus size: 6
56926 TATTTGATAT
* * *
56936 TAAATA TAAATG TATATA TAAGTA TAAATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
56984 T-AATA TAAATA TAAATA TAAATA T
1 TAAATA TAAATA TAAATA TAAATA T
57008 GTAGGATGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
5 5 0.08
6 54 0.92
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:58374 original size:90 final size:88
Alignment explanation
Indices: 58259--58428 Score: 304
Period size: 90 Copynumber: 1.9 Consensus size: 88
58249 TCCCGAATAT
*
58259 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
58324 GGTAACTTGGATATAAGAGGATTA
65 GGTAACTTGGATATAAGAGGATTA
58348 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
58413 GGTAACTTGGCTATAA
65 GGTAACTTGGATATAA
58429 AAGAGTGTGT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 37 0.47
90 41 0.53
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAGAGGATTA
Found at i:65230 original size:90 final size:89
Alignment explanation
Indices: 65119--65291 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
65109 TAATCCCGAA
*
65119 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCATAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCATAATATGAT
65184 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGTAACTTGGATATAAGAGGAT
* *
65209 TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
*
65274 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
65292 AAGAGTGTGT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (89 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:70321 original size:54 final size:54
Alignment explanation
Indices: 70229--70681 Score: 478
Period size: 54 Copynumber: 8.5 Consensus size: 54
70219 TGCATTTTTA
* *
70229 TGTATCGACACTAAGTGTGCAACCCACATATTTCATAATAAGTTTATGAACAAC
1 TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAAC
* * **
70283 TATATCGACACTAAGTGTGCAACCCACAGAATTTATAATAAGTTTATGAATGAC
1 TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAAC
* * * * * *
70337 CGTATCGGCGCTACGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACC
1 TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAAC-AAC
70392 T-TATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAA-AGAC
1 TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACA-AC
* * * ** *
70445 TGTATCGGCACTAAGTGTGCAATCCACAAAATGT-ATACCAAGTTTATGAACGAC
1 TGTATCGACACTAAGTGTGCAACCCACAGAAT-TCATAATAAGTTTATGAACAAC
* * **
70499 CGTATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAAC-GG
1 TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAAC
* * *
70552 TCGTATTTG-TACTAAGTGTGTAACCCAC-GTAATTCATAATAAGTTTAT-AACAAC
1 T-GTA-TCGACACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACAAC
* ** ** *
70606 CGTAT---CAC-AAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGAT
1 TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAAC
* *
70656 TGTATCGGCACTAAGTGTGCACCCCA
1 TGTATCGACACTAAGTGTGCAACCCA
70682 TGAAACTTAT
Statistics
Matches: 330, Mismatches: 53, Indels: 32
0.80 0.13 0.08
Matches are distributed among these distances:
49 31 0.09
50 10 0.03
52 2 0.01
53 13 0.04
54 270 0.82
55 4 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
TGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAAC
Found at i:70419 original size:108 final size:108
Alignment explanation
Indices: 70230--70681 Score: 558
Period size: 108 Copynumber: 4.2 Consensus size: 108
70220 GCATTTTTAT
* * * * **
70230 GTATCGACACTAAGTGTGCAACCCACATATTTCATAATAAGTTTATGAACAACTATATCGACACT
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGACACT
*
70295 AAGTGTGCAACCCACAGAATTTATAATAAGTTTATGAATGACC
66 AAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACC
* * * *
70338 GTATCGGCGCTACGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACCTTATCGACACT
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGACACT
* *
70403 AAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAAAGACT
66 AAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACC
* * **
70446 GTATCGGCACTAAGTGTGCAATCCACAAAATGT-ATACCAAGTTTATGAACGACCGTATCGACAC
1 GTATCGGCACTAAGTGTGCAACCCACAGAAT-TCATAATAAGTTTATGAACGACCGTATCGACAC
* * **
70510 TAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGGTC
65 TAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACC
** * * *
70554 GTATTTGTACTAAGTGTGTAACCCAC-GTAATTCATAATAAGTTTAT-AACAACCGTAT---CAC
1 GTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCGTATCGACAC
** **
70614 -AAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAATGATT
65 TAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACC
*
70657 GTATCGGCACTAAGTGTGCACCCCA
1 GTATCGGCACTAAGTGTGCAACCCA
70682 TGAAACTTAT
Statistics
Matches: 298, Mismatches: 43, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
103 59 0.20
104 3 0.01
107 11 0.04
108 224 0.75
109 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (108 bp):
GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGACACT
AAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACC
Found at i:70602 original size:27 final size:27
Alignment explanation
Indices: 70528--70602 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 27
70518 CAACCCATAG
***
70528 AATTCATAATAAGTTTATGAACGGTCGT
1 AATTCATAATAAGTTTAT-AACCCACGT
** * * *
70556 -ATTTGTACTAAGTGTGTAACCCACGT
1 AATTCATAATAAGTTTATAACCCACGT
70582 AATTCATAATAAGTTTATAAC
1 AATTCATAATAAGTTTATAAC
70603 AACCGTATCA
Statistics
Matches: 33, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
26 6 0.18
27 27 0.82
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (27 bp):
AATTCATAATAAGTTTATAACCCACGT
Done.