Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000056.1 Hibiscus syriacus cultivar Beakdansim tig00000083_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: 75850
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6872 original size:6 final size:6
Alignment explanation
Indices: 6855--6898 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
6845 AGCCATAATA
* * *
6855 TATATT TGTATT TATATT TATACT TACATT TATATT TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TA
6899 ATAACAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:6991 original size:47 final size:51
Alignment explanation
Indices: 6940--7035 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 51
6930 CATTAATCAT
*
6940 ATATAACTTACACATATAAC-AT-ATATTAA-ATATAT-ATATATTTACGC
1 ATATAACCTACACATATAACAATAATATTAATATATATAATATATTTACGC
* * *
6987 ATATAACCTATATATTTAACAATCAATATTAATATATATAATATATTTA
1 ATATAACCTACACATATAACAAT-AATATTAATATATATAATATATTTA
7036 GTGACAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 16 0.40
48 2 0.05
50 7 0.17
51 6 0.15
52 9 0.22
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (51 bp):
ATATAACCTACACATATAACAATAATATTAATATATATAATATATTTACGC
Found at i:13829 original size:286 final size:285
Alignment explanation
Indices: 13270--13829 Score: 797
Period size: 286 Copynumber: 2.0 Consensus size: 285
13260 AAGAATTTTT
* * * **
13270 TGTCTAACGCTTTGATCCTAGTGGCATCGATCCTTGATAGACCGATAATTTTCTACCTGACGGTC
1 TGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACCGATAATCCTCTACCTGACGGTC
* *
13335 TTTGAGAATTCAATGGGATATGTGCTGGGACAACATGATGAATCTGAAAAGAATGAAAGAGTCAT
66 TTTGAGAATTCAATGGGATATGTGCTGGGACAACAAGATGAATCTGAAAAGAAGGAAAGAGTCAT
* * * *
13400 TTATTATTTGAGTAAAAAGTTCACTGATTGCGGGATCTGGTACCTCCCAATTCATAAGCCATGTT
131 TTACTATTTGAGTAAAAAGTTCACTGATTGCGAGATCCGGTACCCCCCAATTCATAAGCCATGTT
**
13465 GTGCTTTGGTATAGGATACCAAGAGGCTAAATTAGTATATGATATACCATACCACTTGGATGATA
196 GTGCTTTGGTATAGGATACCAAGAGGCTAAAGAAGTATATGATATACCATACCACTTGGATGATA
13530 TCCAAACTCGATCCTTTGAAATTTC
261 TCCAAACTCGATCCTTTGAAATTTC
13555 TGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACC-ATTAATCCTCTACCTGACGGT
1 TGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACCGA-TAATCCTCTACCTGACGGT
* * *
13619 CTTTGATAATTCAATAGGGATGTGTGTTGGGACAACAAGATGAATCTGGAAAA-AAGGAAAG-GA
65 CTTTGAGAATTCAAT-GGGATATGTGCTGGGACAACAAGATGAATCT-GAAAAGAAGGAAAGAG-
* * * *
13682 TCATTTACTA-TTGAGTAAAAATTTCACTGATTGCGAGATCCGGTACCCCCCAAATTTATAATCT
127 TCATTTACTATTTGAGTAAAAAGTTCACTGATTGCGAGATCCGGTACCCCCC-AATTCATAAGCC
* * * * * *
13746 ATGTTTTGCTTTGGTATGGGATACCAAGGGGCTCAAGAAGTATATGTTATACCATACCACTTGGC
191 ATGTTGTGCTTTGGTATAGGATACCAAGAGGCTAAAGAAGTATATGATATACCATACCACTTGGA
13811 TGATATCCAGAA-TCGATCC
256 TGATATCCA-AACTCGATCC
13830 CCTTAAGTTC
Statistics
Matches: 243, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
284 1 0.00
285 109 0.45
286 126 0.52
287 7 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (285 bp):
TGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACCGATAATCCTCTACCTGACGGTC
TTTGAGAATTCAATGGGATATGTGCTGGGACAACAAGATGAATCTGAAAAGAAGGAAAGAGTCAT
TTACTATTTGAGTAAAAAGTTCACTGATTGCGAGATCCGGTACCCCCCAATTCATAAGCCATGTT
GTGCTTTGGTATAGGATACCAAGAGGCTAAAGAAGTATATGATATACCATACCACTTGGATGATA
TCCAAACTCGATCCTTTGAAATTTC
Found at i:16394 original size:20 final size:20
Alignment explanation
Indices: 16366--16404 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16356 TATTCAACCC
* *
16366 GAATCGAGTTAACTCGACCT
1 GAATCGAGTCAACCCGACCT
*
16386 GAATTGAGTCAACCCGACC
1 GAATCGAGTCAACCCGACC
16405 CGACCCGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (20 bp):
GAATCGAGTCAACCCGACCT
Found at i:16459 original size:22 final size:24
Alignment explanation
Indices: 16409--16471 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 24
16399 CCGACCCGAC
16409 CCGTTGACTTTGATCTGAGTCGTTAA
1 CCGTTGACTTTGA-CTGAGTC-TTAA
*
16435 CCGTTGACTTTGACT-AGT-TTGA
1 CCGTTGACTTTGACTGAGTCTTAA
16457 CCGTTGACTTTGACT
1 CCGTTGACTTTGACT
16472 TTGACAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 18 0.50
24 3 0.08
25 2 0.06
26 13 0.36
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (24 bp):
CCGTTGACTTTGACTGAGTCTTAA
Found at i:22329 original size:35 final size:35
Alignment explanation
Indices: 22290--22403 Score: 106
Period size: 35 Copynumber: 3.2 Consensus size: 35
22280 TCAAACTGGT
*
22290 ATTCCTTATATAGGTTCAGACCGATCGAATTAGTA
1 ATTCCTTATATAGGTTCAGACCGATCGAACTAGTA
*** * * *
22325 ATTCCTTACGGCAGGTTCAG-CTCGGTCAAACTGGTA
1 ATTCCTTA-TATAGGTTCAGAC-CGATCGAACTAGTA
* *
22361 ATTCCTTATATAGGTTCAGATCGATCGAGC-AGGTA
1 ATTCCTTATATAGGTTCAGACCGATCGAACTA-GTA
22396 ATTCCTTA
1 ATTCCTTA
22404 CGGATCGAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
35 34 0.57
36 26 0.43
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (35 bp):
ATTCCTTATATAGGTTCAGACCGATCGAACTAGTA
Found at i:22388 original size:71 final size:70
Alignment explanation
Indices: 22266--22406 Score: 203
Period size: 71 Copynumber: 2.0 Consensus size: 70
22256 GAAGTCTCTA
* * **
22266 CAGGTTTAGCTCTATCAAACTGGTATTCCTTATATAGGTTCAGACCGATCGAATTA-GTAATTCC
1 CAGGTTCAGCTCGATCAAACTGGTATTCCTTATATAGGTTCAGACCGATCG-AGCAGGTAATTCC
22330 TTACGG
65 TTACGG
* *
22336 CAGGTTCAGCTCGGTCAAACTGGTAATTCCTTATATAGGTTCAGATCGATCGAGCAGGTAATTCC
1 CAGGTTCAGCTCGATCAAACTGGT-ATTCCTTATATAGGTTCAGACCGATCGAGCAGGTAATTCC
22401 TTACGG
65 TTACGG
22407 ATCGAATGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
70 23 0.37
71 40 0.63
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (70 bp):
CAGGTTCAGCTCGATCAAACTGGTATTCCTTATATAGGTTCAGACCGATCGAGCAGGTAATTCCT
TACGG
Found at i:23489 original size:13 final size:13
Alignment explanation
Indices: 23471--23496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23461 TAAATATAAG
23471 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
23484 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
23497 GAAAATTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:23490 original size:11 final size:11
Alignment explanation
Indices: 23468--23501 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
23458 CAATAAATAT
23468 AAGAAGAAAAA
1 AAGAAGAAAAA
23479 AAGAAAAGAAAAA
1 AAG--AAGAAAAA
23492 AAGAAGAAAA
1 AAGAAGAAAA
23502 TTAAGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:23493 original size:16 final size:16
Alignment explanation
Indices: 23468--23501 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23458 CAATAAATAT
*
23468 AAGAAGAAAAAAAGAA
1 AAGAAAAAAAAAAGAA
*
23484 AAGAAAAAAAGAAGAA
1 AAGAAAAAAAAAAGAA
23500 AA
1 AA
23502 TTAAGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAGAA
Found at i:24752 original size:78 final size:77
Alignment explanation
Indices: 24520--24761 Score: 231
Period size: 76 Copynumber: 3.1 Consensus size: 77
24510 TTAAGGGGAC
* *
24520 AAGTTCATAATGAGAATAACTTGTTCAACCTTTGCTCAATTCCATCACATA-AAGAGT-TGGATC
1 AAGTTCATAATGAGAAGAACTTGTTCAACC-TTGCT-AA-TCCAT-A-ATAGAAGAATGTGGATC
* * *
24583 ATCATTTCTAGGAGAAG
61 AACATTTCCAAGAGAAG
* * * * * * * *
24600 AAGTTCATAATAAAAAGAACTTGTTCAACCCT-CTCATCCATCACAGAATG-AGGTGGGTCAACA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTGCTAATCCATAATAGAA-GAATGTGGATCAACA
*
24663 TTTCCAAGAGAAA
65 TTTCCAAGAGAAG
* * *
24676 AAGTTCATGATGAGAAGAACTTGTTCAACCTTGACTTATCCATAATAGAAGAATGTAGATCAACA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTG-CTAATCCATAATAGAAGAATGTGGATCAACA
24741 TTTCCAAGAGAAG
65 TTTCCAAGAGAAG
*
24754 AATTTCAT
1 AAGTTCAT
24762 TATAAGAACT
Statistics
Matches: 130, Mismatches: 26, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
74 2 0.02
75 2 0.02
76 52 0.40
77 2 0.02
78 44 0.34
79 1 0.01
80 27 0.21
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (77 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTGCTAATCCATAATAGAAGAATGTGGATCAACAT
TTCCAAGAGAAG
Found at i:25048 original size:78 final size:78
Alignment explanation
Indices: 24911--25057 Score: 249
Period size: 78 Copynumber: 1.9 Consensus size: 78
24901 TAGCTCAAGG
* * *
24911 AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATTAGAAGAACTTGTTCAACCTTGACTCAT
1 AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
24976 CCATCACAGAAGA
66 CCATCACAGAAGA
* *
24989 AGGTGGATCAACATTTCCAAGAGAATAATTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
1 AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
25054 CCAT
66 CCAT
25058 AAAAAAAGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (78 bp):
AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
CCATCACAGAAGA
Found at i:30078 original size:22 final size:22
Alignment explanation
Indices: 30050--30103 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
30040 AACCCGAAAT
30050 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
30072 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
30094 AATAAAAATA
1 AATAAAAATA
30104 ATAATTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAAAAATATTATTTTTATTC
Found at i:46531 original size:1 final size:1
Alignment explanation
Indices: 46525--46602 Score: 57
Period size: 1 Copynumber: 78.0 Consensus size: 1
46515 TCCTAAGTTG
* * * * * * * * * *
46525 AAAAAAAAAAAACAAAACAAAACAAAAAAAACAAAACAAAACAAAACAAAACAAAAAAACAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
46590 AAAAAAACAAAAA
1 AAAAAAAAAAAAA
46603 GGGAAGAACG
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:46553 original size:19 final size:19
Alignment explanation
Indices: 46525--46601 Score: 108
Period size: 19 Copynumber: 4.2 Consensus size: 19
46515 TCCTAAGTTG
46525 AAAA-AAAAAAAACAAAAC
1 AAAACAAAAAAAACAAAAC
46543 AAAACAAAAAAAACAAAAC
1 AAAACAAAAAAAACAAAAC
46562 AAAACAAAACAAAAC-AAA-
1 AAAACAAAA-AAAACAAAAC
*
46580 AAAACAAAACAAA-AAAAC
1 AAAACAAAAAAAACAAAAC
46598 AAAA
1 AAAA
46602 AGGGAAGAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
17 6 0.11
18 17 0.31
19 26 0.48
20 5 0.09
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAAAACAAAAC
Found at i:46677 original size:1 final size:1
Alignment explanation
Indices: 46642--46667 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
46632 AGGGCACCCT
46642 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
46668 GAGGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:47593 original size:105 final size:105
Alignment explanation
Indices: 47411--47977 Score: 890
Period size: 105 Copynumber: 5.4 Consensus size: 105
47401 AGGTTTTACC
*
47411 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
47476 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
47516 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
47581 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAA-TT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATTT
* * *
47621 CAAGAGCCAATTTCAATTTCAAAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
47686 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTT
* *
47728 -AGAGCCAATTTCAACGTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
47792 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATTT
*
47833 -AGAGCCAATTTCAACTTCACAACGAAGGATATTGGTCTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
47897 ACGAAGGGACCACTGGTTGTCAACGAATCATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAAC-AAACATTTCTCAATTT
* * *
47938 CAGAACCGATTTCAACTTCACAGC-AGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGA-AGGATATTGGACTC
47978 GGAACAATAC
Statistics
Matches: 429, Mismatches: 25, Indels: 15
0.91 0.05 0.03
Matches are distributed among these distances:
105 287 0.67
106 140 0.33
107 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:47776 original size:211 final size:209
Alignment explanation
Indices: 47412--47977 Score: 900
Period size: 211 Copynumber: 2.7 Consensus size: 209
47402 GGTTTTACCC
*
47412 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
47477 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGA
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAATTT-AGAGCCAATTTCAACTTCACAGCGA
*
47542 AGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
130 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
47607 ACATTTCTCCAATTCA
195 ACATTTCTCCAATT-A
* * *
47623 AGAGCCAATTTCAATTTCAAAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
47688 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTTAGAGCCAATTTCAACGTCACAGCGA
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTC-AATTTAGAGCCAATTTCAACTTCACAGCGA
*
47753 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAA
130 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
47818 ACATTTCTCCAATTT
195 ACATTTCTCCAATTA
*
47833 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGTCTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * * * * * *
47898 CGAAGGGACCACTGGTTGTCAACGAATCATTTCCCAGTTCCAGAACCGATTTCAACTTCACAGC-
66 CGAAGGGACCGCTGGTTGTC-ACCAAACATTTCTCAATT-TAGAGCCAATTTCAACTTCACAGCG
47962 AGAGGATATTGGACTC
129 A-AGGATATTGGACTC
47978 GGAACAATAC
Statistics
Matches: 328, Mismatches: 23, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
210 84 0.26
211 239 0.73
212 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (209 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAATTTAGAGCCAATTTCAACTTCACAGCGAA
GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
CATTTCTCCAATTA
Found at i:49701 original size:13 final size:12
Alignment explanation
Indices: 49653--49703 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
49643 CATTTTGTAT
49653 TTTATCTTATTA
1 TTTATCTTATTA
* * *
49665 TTTCT-TTACTC
1 TTTATCTTATTA
49676 TTT-TCTTATTA
1 TTTATCTTATTA
49687 TTTATCTTCATTA
1 TTTATCTT-ATTA
49700 TTTA
1 TTTA
49704 GTTTTTCCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 14 0.45
12 8 0.26
13 8 0.26
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATCTTATTA
Found at i:50001 original size:29 final size:29
Alignment explanation
Indices: 49968--50026 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
49958 TTTATTTTAG
*
49968 TTTTTTTTTATTAC-TATTATATATATCT
1 TTTTTTTTTTTTACTTATTATATATATCT
* *
49996 TTTTTTTTTTTTACTTTTTTTATATATCT
1 TTTTTTTTTTTTACTTATTATATATATCT
50025 TT
1 TT
50027 ATTATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTTTTTTTTTACTTATTATATATATCT
Found at i:52649 original size:18 final size:17
Alignment explanation
Indices: 52617--52654 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
52607 TAATCATAGA
52617 TAGAATTTTAACTTAGC
1 TAGAATTTTAACTTAGC
*
52634 TAGAACTTTTACCTTAGC
1 TAGAA-TTTTAACTTAGC
52652 TAG
1 TAG
52655 GACTCTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (17 bp):
TAGAATTTTAACTTAGC
Found at i:55844 original size:23 final size:23
Alignment explanation
Indices: 55807--55916 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 23
55797 CAGCTCGTAT
*
55807 AAATGCACCGAAGTGCCACATAG
1 AAATGCACTGAAGTGCCACATAG
* * * *
55830 AATTGCACTGTAGTGCCGCGTAG
1 AAATGCACTGAAGTGCCACATAG
55853 AAATGCA-TCGAAGTGCCACATAG
1 AAATGCACT-GAAGTGCCACATAG
* * * *
55876 AATTGCACTGTAGTGCCGCGTAG
1 AAATGCACTGAAGTGCCACATAG
*
55899 AAATGCACCGAAGTGCCA
1 AAATGCACTGAAGTGCCA
55917 TATAAGATGT
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
22 1 0.01
23 66 0.97
24 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (23 bp):
AAATGCACTGAAGTGCCACATAG
Found at i:55874 original size:46 final size:46
Alignment explanation
Indices: 55802--55916 Score: 212
Period size: 46 Copynumber: 2.5 Consensus size: 46
55792 CACCACAGCT
*
55802 CGTATAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
*
55848 CGTAGAAATGCATCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
55894 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
55917 TATAAGATGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (46 bp):
CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
Found at i:61200 original size:23 final size:23
Alignment explanation
Indices: 61174--61238 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
61164 CACCACAGCT
* *
61174 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGACA
* * * *
61197 CGTAGAATTGCACTGTAGT-ACG
1 CGTAGAAATGCACCGAAGTGACA
61219 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
61239 TCATATAAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGACA
Found at i:67622 original size:33 final size:34
Alignment explanation
Indices: 67566--67633 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
67556 GTGAAACAAT
**
67566 GACAACATCCAAAAATCTGGCATCTCACGGTCAA
1 GACAACATCCAAAAATCCAGCATCTCACGGTCAA
*
67600 GACAACTTCC-AAAATCCAGCATCTCACGGTCAA
1 GACAACATCCAAAAATCCAGCATCTCACGGTCAA
67633 G
1 G
67634 TCATATCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.18
Consensus pattern (34 bp):
GACAACATCCAAAAATCCAGCATCTCACGGTCAA
Found at i:70098 original size:27 final size:27
Alignment explanation
Indices: 70068--70121 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
70058 TAATATGGTA
70068 ATTTTGAAAAT-TTATT-TTTTTAAAAAG
1 ATTTT-AAAATATT-TTATTTTTAAAAAG
70095 ATTTTAAAATATTTTATTTTTAAAAAG
1 ATTTTAAAATATTTTATTTTTAAAAAG
70122 CCCTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (27 bp):
ATTTTAAAATATTTTATTTTTAAAAAG
Done.