Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001439.1 Hibiscus syriacus cultivar Beakdansim tig00002788_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: 69619
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:12222 original size:36 final size:36
Alignment explanation
Indices: 12173--12251 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
12163 TTAATTGAGT
* *
12173 TCAAGCTTGAGTACAAGAATCTGTAAACT-AGCTTAA
1 TCAAGCTTAAGTACAAGAATCTGCAAA-TGAGCTTAA
*
12209 TCAAGCTTAAGTACAAGAATCTGCAAATGAGCTTAG
1 TCAAGCTTAAGTACAAGAATCTGCAAATGAGCTTAA
12245 TCAAGCT
1 TCAAGCT
12252 CAAGCTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (36 bp):
TCAAGCTTAAGTACAAGAATCTGCAAATGAGCTTAA
Found at i:12501 original size:3 final size:3
Alignment explanation
Indices: 12493--12517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12483 AGAGAGAGAG
12493 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
12518 ATATAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:15273 original size:74 final size:75
Alignment explanation
Indices: 15130--15280 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 75
15120 TCTTTTTCTC
* *
15130 CTTCTGTTGATTAAGGAGCTTCTCTATAACTCCTTTAATTAAGAAGGGGGTTTTTAACGAGGCCT
1 CTTCTGTTGATTAAGGAGCTTCTCTATAACTCCTTTAATT-ACAAGGGGGATTTTAACGAGGCCT
15195 TCATTTCCTAT
65 TCATTTCCTAT
15206 CTTCTGCTT-ATTAAGGAGCTTCTCTATAAACTCCTTTAA-T-CAAGGGGGATTTTAACGAGGCC
1 CTTCTG-TTGATTAAGGAGCTTCTCTAT-AACTCCTTTAATTACAAGGGGGATTTTAACGAGGCC
15268 TTCATTTCCTAT
64 TTCATTTCCTAT
15280 C
1 C
15281 AAAAAAAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
74 33 0.46
76 25 0.35
77 13 0.18
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (75 bp):
CTTCTGTTGATTAAGGAGCTTCTCTATAACTCCTTTAATTACAAGGGGGATTTTAACGAGGCCTT
CATTTCCTAT
Found at i:15342 original size:48 final size:48
Alignment explanation
Indices: 15289--15385 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
15279 TCAAAAAAAA
* *
15289 AGTTTAATAATTTATGCTCTTGCACAAGCAGCATTTAAGCTCAATTTC
1 AGTTTAATAATTCATGCTCTTGCACAAGCAGCATTCAAGCTCAATTTC
* * *
15337 AGTTTAATAATTCATGTTCTTGCTCAAGCAGCATTCAAGCTCAGTTTC
1 AGTTTAATAATTCATGCTCTTGCACAAGCAGCATTCAAGCTCAATTTC
15385 A
1 A
15386 TCTCTGGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (48 bp):
AGTTTAATAATTCATGCTCTTGCACAAGCAGCATTCAAGCTCAATTTC
Found at i:21343 original size:28 final size:29
Alignment explanation
Indices: 21293--21351 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
21283 AGGGGTGCAC
21293 AAAAAATCCGAATATCCGATTTTGCGAAA
1 AAAAAATCCGAATATCCGATTTTGCGAAA
* *
21322 AAAAATATCCGAA-A-CCGGTTTTGGGAAA
1 AAAAA-ATCCGAATATCCGATTTTGCGAAA
21350 AA
1 AA
21352 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 14 0.52
29 6 0.22
30 7 0.26
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAAAATCCGAATATCCGATTTTGCGAAA
Found at i:21437 original size:12 final size:12
Alignment explanation
Indices: 21422--21490 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 12
21412 GGTTTTTTAT
21422 CCGGTAAAAAAA
1 CCGGTAAAAAAA
21434 CCGGTTTGAAAAAAA
1 CCGG--T-AAAAAAA
*
21449 CCGGTTAAAAAA
1 CCGGTAAAAAAA
21461 CCGGTTTGAAAAAAA
1 CCGG--T-AAAAAAA
*
21476 CCGGTTAAAAAA
1 CCGGTAAAAAAA
21488 CCG
1 CCG
21491 ATTTTTATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
12 23 0.48
13 2 0.04
14 2 0.04
15 21 0.44
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (12 bp):
CCGGTAAAAAAA
Found at i:21452 original size:27 final size:27
Alignment explanation
Indices: 21422--21490 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
21412 GGTTTTTTAT
*
21422 CCGGTAAAAAAACCGGTTTGAAAAAAA
1 CCGGTTAAAAAACCGGTTTGAAAAAAA
21449 CCGGTTAAAAAACCGGTTTGAAAAAAA
1 CCGGTTAAAAAACCGGTTTGAAAAAAA
21476 CCGGTTAAAAAACCG
1 CCGGTTAAAAAACCG
21491 ATTTTTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (27 bp):
CCGGTTAAAAAACCGGTTTGAAAAAAA
Found at i:21487 original size:15 final size:15
Alignment explanation
Indices: 21427--21481 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
21417 TTTATCCGGT
21427 AAAAAAACCGGTTTG
1 AAAAAAACCGGTTTG
21442 AAAAAAACCGG-TT-
1 AAAAAAACCGGTTTG
21455 -AAAAAACCGGTTTG
1 AAAAAAACCGGTTTG
21469 AAAAAAACCGGTT
1 AAAAAAACCGGTT
21482 AAAAAACCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.27
13 2 0.05
14 2 0.05
15 23 0.62
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (15 bp):
AAAAAAACCGGTTTG
Found at i:21947 original size:21 final size:21
Alignment explanation
Indices: 21923--21962 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21913 TTTATTTTAT
21923 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
21944 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
21963 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:22010 original size:33 final size:33
Alignment explanation
Indices: 21957--22055 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
21947 TTTGTTTCAA
21957 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
21989 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
22022 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
22055 T
1 T
22056 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:22084 original size:13 final size:13
Alignment explanation
Indices: 22041--22095 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
22031 TTGGAAGTAT
22041 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
22054 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
22068 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
22081 TTAAGTATTTGAA
1 TTAAGTATTTCAA
22094 TT
1 TT
22096 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:22520 original size:15 final size:15
Alignment explanation
Indices: 22500--22546 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
22490 ATTAAAATCA
*
22500 GTTTTTTTATAACCG
1 GTTTTTTTAAAACCG
*
22515 GTTTTTTAAAAAAACCG
1 GTTTTTT--TAAAACCG
22532 GTTTTTTTAAAACCG
1 GTTTTTTTAAAACCG
22547 AAACCGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.52
17 13 0.48
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
GTTTTTTTAAAACCG
Found at i:22555 original size:21 final size:18
Alignment explanation
Indices: 22510--22543 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22500 GTTTTTTTAT
22510 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
22527 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
22544 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:23366 original size:27 final size:30
Alignment explanation
Indices: 23336--23395 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 30
23326 ATAGATTTTA
*
23336 TTAAAATTGA-TTATAAATT-TTA-ATAAG
1 TTAAAATTAAGTTATAAATTGTTATATAAG
*
23363 TT-AAATTAAGTTATTAATTGTTATATAAG
1 TTAAAATTAAGTTATAAATTGTTATATAAG
23392 TTAA
1 TTAA
23396 TATATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.22
27 10 0.37
28 3 0.11
29 7 0.26
30 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAAAATTAAGTTATAAATTGTTATATAAG
Found at i:28863 original size:54 final size:55
Alignment explanation
Indices: 28781--28896 Score: 182
Period size: 54 Copynumber: 2.1 Consensus size: 55
28771 TCAGTAACTA
* *
28781 GTTTCCCCTTTTTATTATTTACAGTTGGAGGGAT-TTTTTAGGATAAATTACA-C
1 GTTTCTCCTTTTTATTATTTACAATTGGAGGGATATTTTTAGGATAAATTACATC
*
28834 TGTTTCTCCTTTTTATTATTTACAATTGGAGGGATATTTTTAGGGTAAATTACATC
1 -GTTTCTCCTTTTTATTATTTACAATTGGAGGGATATTTTTAGGATAAATTACATC
28890 GTTTCTC
1 GTTTCTC
28897 ATTAAACTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 32 0.56
55 24 0.42
56 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.47
Consensus pattern (55 bp):
GTTTCTCCTTTTTATTATTTACAATTGGAGGGATATTTTTAGGATAAATTACATC
Found at i:35660 original size:53 final size:54
Alignment explanation
Indices: 35591--35694 Score: 174
Period size: 53 Copynumber: 1.9 Consensus size: 54
35581 TAATTCTGCT
* *
35591 TGGCATGTCATTCTAACGGGCCATCAGCTCGGAC-AATAAATAGTAATTTTGAC
1 TGGCATGTCATTCTAACGGGCAATCAGCTCAGACTAATAAATAGTAATTTTGAC
*
35644 TGGCATGTCATTCTAACGGGCAATCAGCTCAGACTAGTAAATAGTAATTTT
1 TGGCATGTCATTCTAACGGGCAATCAGCTCAGACTAATAAATAGTAATTTT
35695 AGAACCGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 32 0.68
54 15 0.32
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (54 bp):
TGGCATGTCATTCTAACGGGCAATCAGCTCAGACTAATAAATAGTAATTTTGAC
Found at i:38411 original size:20 final size:20
Alignment explanation
Indices: 38388--38429 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
38378 TCTAACACTT
* * *
38388 AAAAGGTTTTGATATTTATG
1 AAAAGGTATCGATATTCATG
38408 AAAAGGTATCGATATTCATG
1 AAAAGGTATCGATATTCATG
38428 AA
1 AA
38430 CGAGTACTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (20 bp):
AAAAGGTATCGATATTCATG
Found at i:46084 original size:30 final size:30
Alignment explanation
Indices: 46012--46095 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
46002 CCCGAAGGAC
* * * *
46012 CTATCCAGAGGTCATACAG-ACCCCGGTAA
1 CTATCCAAAGGTCATAAAGAACCTCGGCAA
46041 CTATCCAAAAGGTCATAAAGAACCTCGGCAA
1 CTATCC-AAAGGTCATAAAGAACCTCGGCAA
* * **
46072 CTGTCCATAGGTCCCAAAGAACCT
1 CTATCCAAAGGTCATAAAGAACCT
46096 AGGTAAATTG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
29 6 0.13
30 26 0.58
31 13 0.29
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.18
Consensus pattern (30 bp):
CTATCCAAAGGTCATAAAGAACCTCGGCAA
Found at i:46111 original size:31 final size:31
Alignment explanation
Indices: 46070--46164 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
46060 GAACCTCGGC
* *
46070 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* * **
46101 AATTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
46132 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
46163 AA
1 AA
46165 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 47 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:46330 original size:17 final size:19
Alignment explanation
Indices: 46298--46333 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
46288 CATATATCTC
46298 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
46317 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
46334 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:46924 original size:63 final size:65
Alignment explanation
Indices: 46814--46961 Score: 187
Period size: 63 Copynumber: 2.3 Consensus size: 65
46804 CTCTTTCATG
* * * *
46814 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTAT-TTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTT-TCTTTA
46877 A
65 A
* * *
46878 AAGG-ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCACTA-CTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCTTTA
46941 A
65 A
46942 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
46962 TATGAATGTG
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
63 44 0.60
64 15 0.21
65 14 0.19
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (65 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTCTTTAA
Found at i:50307 original size:31 final size:31
Alignment explanation
Indices: 50253--50347 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
50243 GAACCTCGGC
* *
50253 AACTGTCCATAGGTCCCAAAGAACCTAAGTA
1 AACTGTCCATATGTCCCAAAGAACATAAGTA
* ** *
50284 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAAGTA
* * *
50315 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAAGTA
50346 AA
1 AA
50348 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
31 48 0.94
32 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAAGTA
Found at i:51107 original size:64 final size:65
Alignment explanation
Indices: 51021--51142 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 65
51011 GAACTACTTG
* * *
51021 TGCATCGGTGCATAAAATGCATTCGATGT-TTTTATTTTAAAAGAATGCATCGATGCATTAGCTA
1 TGCATCGATGCATAAAAGGCATTCGATGTGCTTTATTTTAAAAGAATGCATCGATGCATTAGCTA
* * *
51085 TGCATCGATGCATCAAAGGCATTCGATGTGCTTTCTTTTAAAGGAATGCATCGATGCA
1 TGCATCGATGCATAAAAGGCATTCGATGTGCTTTATTTTAAAAGAATGCATCGATGCA
51143 CTTATGAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
64 26 0.51
65 25 0.49
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (65 bp):
TGCATCGATGCATAAAAGGCATTCGATGTGCTTTATTTTAAAAGAATGCATCGATGCATTAGCTA
Found at i:59004 original size:12 final size:12
Alignment explanation
Indices: 58987--59011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58977 AATCAAAAAG
58987 AAAAATGTTATT
1 AAAAATGTTATT
58999 AAAAATGTTATT
1 AAAAATGTTATT
59011 A
1 A
59012 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAAATGTTATT
Found at i:60412 original size:13 final size:13
Alignment explanation
Indices: 60394--60420 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60384 TTATTAAATA
60394 TTTTAAAATATAT
1 TTTTAAAATATAT
60407 TTTTAAAATATAT
1 TTTTAAAATATAT
60420 T
1 T
60421 ATAATCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:60608 original size:30 final size:28
Alignment explanation
Indices: 60574--60653 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 28
60564 ATTATTTGAG
*
60574 ATTATTTTCTAAAAAAAGTTATTTGTAAAA
1 ATTATTTT-TAAAAAAAGTTATTGGT-AAA
60604 ATTATTTCTTTAAAAAAAAGTT-TTGGTAAA
1 ATTA-TT-TTT-AAAAAAAGTTATTGGTAAA
*
60634 ATTATTTTTAAAAAGAGTTA
1 ATTATTTTTAAAAAAAGTTA
60654 GGTGCCTCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 9 0.20
28 3 0.07
29 2 0.05
30 11 0.25
31 7 0.16
32 12 0.27
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (28 bp):
ATTATTTTTAAAAAAAGTTATTGGTAAA
Found at i:60857 original size:34 final size:30
Alignment explanation
Indices: 60818--60886 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
60808 TTGATATAAC
60818 AATTTAAGGCAAAATGGGTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GGTTTTGGACTT-AATTA
* *
60852 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGGTTTTGGACTTAATTA
60881 AATTTA
1 AATTTA
60887 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 11 0.34
31 6 0.19
33 1 0.03
34 5 0.16
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGGTTTTGGACTTAATTA
Found at i:60897 original size:29 final size:30
Alignment explanation
Indices: 60827--60886 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
60817 CAATTTAAGG
*
60827 CAAAATGGGTTTTGGACTTGAATTAAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
*
60858 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
60887 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:61021 original size:22 final size:23
Alignment explanation
Indices: 60966--61043 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 23
60956 AGGGTGTCAA
*
60966 AGTGCATCCATGCACTCCTG--C-
1 AGTGCATCCATGCAC-CATGCACT
*
60987 AGTGTATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
61009 AGTGCATCGATGCACCATG--C-
1 AGTGCATCCATGCACCATGCACT
61029 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
61044 TCAAACACCG
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.04
20 15 0.31
21 16 0.33
22 14 0.29
23 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:63744 original size:29 final size:30
Alignment explanation
Indices: 63675--63733 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
63665 ACAATTAAGG
*
63675 CAAAATGGTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
63705 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
63734 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:63839 original size:21 final size:21
Alignment explanation
Indices: 63813--63870 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
63803 AGGGTGTCAA
* *
63813 AGTGCATCCATACACCCTTGC
1 AGTGCATCCATGCACCCATGC
*
63834 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
63855 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
63871 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:63860 original size:13 final size:13
Alignment explanation
Indices: 63844--63868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63834 AGTGCATCCA
63844 TGCATCCATGCAG
1 TGCATCCATGCAG
63857 TGCATCCATGCA
1 TGCATCCATGCA
63869 CCTGCACTAG
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:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:63883 original size:22 final size:20
Alignment explanation
Indices: 63813--63894 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 20
63803 AGGGTGTCAA
* *
63813 AGTGCATCCATACACCCTTGC
1 AGTGCATCCATGCA-CCATGC
63834 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCA-CCATGC
63855 AGTGCATCCATGCACC-TGCAC
1 AGTGCATCCATGCACCATG--C
*
63876 TAGTGCATCGATGCACCAT
1 -AGTGCATCCATGCACCAT
63895 ATCCATGCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 33 0.62
22 15 0.28
23 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:64090 original size:22 final size:20
Alignment explanation
Indices: 64060--64120 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
64050 TTTGAGTAGA
64060 AAAATCATCCCCAAAACGGCTCT
1 AAAA-CATCCCC--AACGGCTCT
*
64083 AAAACATCCTCAACGGCTCT
1 AAAACATCCCCAACGGCTCT
*
64103 AAAACATCCTCAACGGCT
1 AAAACATCCCCAACGGCT
64121 ATATACAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 27 0.73
22 6 0.16
23 4 0.11
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (20 bp):
AAAACATCCCCAACGGCTCT
Found at i:64099 original size:20 final size:20
Alignment explanation
Indices: 64074--64120 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
64064 TCATCCCCAA
64074 AACGGCTCTAAAACATCCTC
1 AACGGCTCTAAAACATCCTC
64094 AACGGCTCTAAAACATCCTC
1 AACGGCTCTAAAACATCCTC
64114 AACGGCT
1 AACGGCT
64121 ATATACAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (20 bp):
AACGGCTCTAAAACATCCTC
Done.