Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002975.1 Hibiscus syriacus cultivar Beakdansim tig00006154_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: 71579
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:6210 original size:23 final size:23
Alignment explanation
Indices: 6183--6227 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
6173 AACTCCATCA
*
6183 CCTCTCCCAAGGGTATTTCATTT
1 CCTCTCCCAAAGGTATTTCATTT
6206 CCTCTCCCAAAGGTATTTCATT
1 CCTCTCCCAAAGGTATTTCATT
6228 GCGTCATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.38
Consensus pattern (23 bp):
CCTCTCCCAAAGGTATTTCATTT
Found at i:12032 original size:35 final size:36
Alignment explanation
Indices: 11960--12034 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
11950 AAAAGTCTGT
*
11960 AATTTCATTCTAAACCCCAAATTCCAAAAATAATTC
1 AATTACATTCTAAACCCCAAATTCCAAAAATAATTC
* * * *
11996 AATTACATTTTAAACCTCAAATT-CTAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCCAAAAATAATTC
12031 AATT
1 AATT
12035 TAGAGTTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 14 0.41
36 20 0.59
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (36 bp):
AATTACATTCTAAACCCCAAATTCCAAAAATAATTC
Found at i:14864 original size:2 final size:2
Alignment explanation
Indices: 14857--14882 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14847 CCTATTTATC
14857 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
14883 TGATATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22023 original size:41 final size:40
Alignment explanation
Indices: 21959--22476 Score: 436
Period size: 41 Copynumber: 12.7 Consensus size: 40
21949 GGTTCATCGA
* * *
21959 TAGTGGCGTTTTT-TCAACAAACGCCACAAAAGAGTAGTACTT
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTA-TACTT
*
22001 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-ATACTT
* * * *
22042 TAGTGGCATTTTTATACAAACGTCGCTATAGAATTATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAG-ACTATACTT
* * * * *
22083 TAGTGGCGTTTTTATACAAACG-CGTTATACACATGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TATACTT
* *
22123 TAGTGGCGTTTGTGT-TACAAACGCCGCTAAAGACTCTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTATACTT
*
22164 TAGTGGC-ATTTTATACAAA--CCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-ATACTT
* **
22202 TAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TATACTT
* * * * * * *
22243 TAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TATACTT
* * * * *
22284 TAGTGGCGTTTGTGTGTACAAATGTCGCTAAAGACTCGTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACT-ATACTT
* *
22327 TAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-ATACTT
* * * *
22368 TATTGACATTTTTATACAAACACCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-ATACTT
* * * * *
22409 TAGTGGCGTTTTTATTCAAACGCCGCTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TATACTT
* *
22450 TAGTGGCGTTTGTAACACAAACGCCGC
1 TAGTGGCGTTT-TTATACAAACGCCGC
22477 AAGTTTACAA
Statistics
Matches: 391, Mismatches: 67, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
37 12 0.03
38 12 0.03
39 19 0.05
40 24 0.06
41 255 0.65
42 40 0.10
43 29 0.07
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (40 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTATACTT
Found at i:22054 original size:82 final size:82
Alignment explanation
Indices: 21959--22476 Score: 480
Period size: 82 Copynumber: 6.3 Consensus size: 82
21949 GGTTCATCGA
* * *
21959 TAGTGGCGTTTTT-TCAACAAACGCCACAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACG
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACG
* *
22023 CCGCTAAAGACTCATAATT
64 CCGCTAAAGACTCGTACTT
* * * *
22042 TAGTGGCATTTTTATACAAACGTCGCTATAGAATTA-TACTTTAGTGGCGTTTTTATACAAACG-
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAG-ACTAGTACTTTAGTGGCGTTTTTATACAAACGC
* * * *
22105 CGTTATACACAT-GTACTA
65 CGCTAAAGAC-TCGTACTT
* * *
22123 TAGTGGCGTTTGTGT-TACAAACGCCGCTAAAGACT-CTAATTTAGTGGC-ATTTTATACAAA--
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACG
*
22183 CCGCTAAAGACTCATACTT
64 CCGCTAAAGACTCGTACTT
* ** * *
22202 TAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCC
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCC
* * * * *
22267 GTTATACACTTGTACTA
66 GCTAAAGACTCGTACTT
* * * * * *
22284 TAGTGGCGTTTGTGTGTACAAATGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACG
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACG
22349 CCGCTAAAGACTCGTACTT
64 CCGCTAAAGACTCGTACTT
* * * * *
22368 TATTGACATTTTTATACAAACACCGCTAAAGACTCA-TACTTTAGTGGCGTTTTTATTCAAACGC
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-AGTACTTTAGTGGCGTTTTTATACAAACGC
* * * *
22432 CGCTATACACTTGTACTA
65 CGCTAAAGACTCGTACTT
* *
22450 TAGTGGCGTTTGTAACACAAACGCCGC
1 TAGTGGCGTTT-TTATACAAACGCCGC
22477 AAGTTTACAA
Statistics
Matches: 350, Mismatches: 68, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
77 1 0.00
78 20 0.06
79 33 0.09
80 21 0.06
81 33 0.09
82 145 0.41
83 30 0.09
84 67 0.19
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (82 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCC
GCTAAAGACTCGTACTT
Found at i:22387 original size:166 final size:164
Alignment explanation
Indices: 21999--22476 Score: 705
Period size: 166 Copynumber: 2.9 Consensus size: 164
21989 AGAGTAGTAC
* *
21999 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACG
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAAC-
* * * * *
22064 T-CGCTATAGAATTATACTTTAGTGGCGTTTTTATACAAACG-CGTTATACACATGTACTATAGT
65 TCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATTCAAACGCCGTTATACACTTGTACTATAGT
22127 GGCGTTTGTGTTACAAACGCCGCTAAAGACTCTAA
130 GGCGTTTGTGTTACAAACGCCGCTAAAGACTCTAA
*
22162 TTTAGTGGCA-TTTTATACAAA--CCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACT
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACT
* * *
22224 CCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTG
66 CCGCTAAAGACTCATACTTTAGTGGCGTTTTTATTCAAACGCCGTTATACACTTGTACTATAGTG
* *
22289 GCGTTTGTGTGTACAAATGTCGCTAAAGACTCGTAA
131 GCGTTTGTGT-TACAAACGCCGCTAAAGACTC-TAA
* * * *
22325 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTTTATTGACATTTTTATACAAACA
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACT
*
22390 CCGCTAAAGACTCATACTTTAGTGGCGTTTTTATTCAAACGCCGCTATACACTTGTACTATAGTG
66 CCGCTAAAGACTCATACTTTAGTGGCGTTTTTATTCAAACGCCGTTATACACTTGTACTATAGTG
***
22455 GCGTTTGTAACACAAACGCCGC
131 GCGTTTGTGTTACAAACGCCGC
22477 AAGTTTACAA
Statistics
Matches: 281, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
159 1 0.00
160 71 0.25
161 32 0.11
162 30 0.11
163 22 0.08
164 11 0.04
165 9 0.03
166 105 0.37
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (164 bp):
TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACT
CCGCTAAAGACTCATACTTTAGTGGCGTTTTTATTCAAACGCCGTTATACACTTGTACTATAGTG
GCGTTTGTGTTACAAACGCCGCTAAAGACTCTAA
Found at i:25844 original size:43 final size:43
Alignment explanation
Indices: 25779--26043 Score: 250
Period size: 43 Copynumber: 6.1 Consensus size: 43
25769 TAATTAGCGA
* * * *
25779 CGTTTGTATCCAAAAACGCCGTTATAGGTCTGACTTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
* * * * *
25822 CGTTTGTGTTCAAAAACACCGTTATAGGTCTAACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
*
25865 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
* * * * * * *
25908 CGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGG
* *
25952 CGTTTAT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGG
* * *
25995 TGTTT-TGTTCAAAAAACGCCG-TAATAGATATTGA-CTTATTGCGG
1 CGTTTGTG-TCCAAAAACGCCGCT-ATAGAT-CTGACCTT-TTGCGG
26039 CGTTT
1 CGTTT
26044 TTTGTTCTCA
Statistics
Matches: 187, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.01
43 137 0.73
44 47 0.25
45 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (43 bp):
CGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
Found at i:26012 original size:87 final size:85
Alignment explanation
Indices: 25787--26023 Score: 289
Period size: 86 Copynumber: 2.7 Consensus size: 85
25777 GACGTTTGTA
* * * * *
25787 TCCAAAAACGCCGTTATAGGTCTGACTTTTTGCGGCGTTTGTGTTCAAAAACACCGTTATAGGTC
1 TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTT-TGTTCAAAAACGCCGCTATAGATC
*
25852 TAACCTTTTGCGGCGTTTGTG
65 TAACCTTTTGCGGCGTTTATG
* * *
25873 TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTTTTCTAGAAACGCCGCTATATATC
1 TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTGTTC-AAAAACGCCGCTATAGATC
*
25938 ATAACTTTTTGCGGCGTTTAT-
65 -TAACCTTTTGCGGCGTTTATG
* * *
25959 TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGTGTTTTGTTCAAAAAACGCCG-TAATAGA
1 TCCAAAAACGCCGCTATAGGTCT-GACCTTTTGCGGCGTTTTGTTC-AAAAACGCCGCT-ATAGA
26023 T
63 T
26024 ATTGACTTAT
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
85 4 0.03
86 74 0.57
87 52 0.40
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (85 bp):
TCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTGTTCAAAAACGCCGCTATAGATCT
AACCTTTTGCGGCGTTTATG
Found at i:35427 original size:13 final size:13
Alignment explanation
Indices: 35409--35438 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35399 AAAATTTTTG
*
35409 AAAATTTTAATTT
1 AAAATTCTAATTT
35422 AAAATTCTAATTT
1 AAAATTCTAATTT
35435 AAAA
1 AAAA
35439 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATTCTAATTT
Found at i:36782 original size:21 final size:21
Alignment explanation
Indices: 36745--36789 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
36735 GATTTCTGGG
*
36745 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
36766 CAAGGGGAA-CTGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
36787 CAA
1 CAA
36790 ACGGACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:38557 original size:103 final size:103
Alignment explanation
Indices: 38378--38598 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
38368 GGGTCTACGC
* *
38378 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
38443 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
38481 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
38546 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
38584 AGTCCTT-ATGGACAT
1 GGTCCTTCA-GGACAT
38599 TATTATATGG
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 110 0.99
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:38640 original size:23 final size:23
Alignment explanation
Indices: 38607--38669 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
38597 ATTATTATAT
38607 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
38630 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
38653 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
38670 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:42292 original size:21 final size:21
Alignment explanation
Indices: 42254--42298 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42244 GATTTCTGGG
* **
42254 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGACACCCATT
*
42275 CAAGGGGAACCGACACCCCTT
1 CAAGGGGAACCGACACCCATT
42296 CAA
1 CAA
42299 ACGGACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGACACCCATT
Found at i:47619 original size:23 final size:22
Alignment explanation
Indices: 47571--47619 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
47561 CCAGAATGTC
47571 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
47592 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
47615 AAGGA
1 AAGGA
47620 AAATTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:48459 original size:18 final size:18
Alignment explanation
Indices: 48436--48471 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
48426 AGGAATGATA
*
48436 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCAGGACAT
48454 TGTGGTCCTTCAGGACAT
1 TGTGGTCCTTCAGGACAT
48472 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCAGGACAT
Found at i:48527 original size:121 final size:121
Alignment explanation
Indices: 48313--48575 Score: 458
Period size: 121 Copynumber: 2.2 Consensus size: 121
48303 GTCGAGGGTC
* *
48313 TATGTGGTCCTTCGGGATATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAA
1 TATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAA
48378 GTCTGGTGAGACACATACTTGATCCCTAGCATATGTAT-ATGA-TTCTTAAGGAATGA
66 GTCTGGTGAGACACATACTTGATCCCTAGCATATGTATAAT-ACTT-TTAAGGAATGA
48434 TATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAA
1 TATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAA
48499 GTCTGGTGAGACACATACTTGATCCCTAGCATATGTATAATACTTTTAAGGAATGA
66 GTCTGGTGAGACACATACTTGATCCCTAGCATATGTATAATACTTTTAAGGAATGA
**
48555 TATGTGGTCCTTATGGACATT
1 TATGTGGTCCTTCGGGACATT
48576 ATTATATGGC
Statistics
Matches: 136, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
121 132 0.97
122 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (121 bp):
TATGTGGTCCTTCGGGACATTGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAA
GTCTGGTGAGACACATACTTGATCCCTAGCATATGTATAATACTTTTAAGGAATGA
Found at i:48532 original size:59 final size:59
Alignment explanation
Indices: 48348--48532 Score: 152
Period size: 59 Copynumber: 3.1 Consensus size: 59
48338 TCCTTCGGGA
48348 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
* * * * * * *
48407 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCCCT
48464 CAGG
58 -A-G
48468 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
48528 CATAT
1 CATAT
48533 GTATAATACT
Statistics
Matches: 93, Mismatches: 14, Indels: 38
0.64 0.10 0.26
Matches are distributed among these distances:
57 6 0.06
58 7 0.08
59 24 0.26
60 12 0.13
61 12 0.13
62 19 0.20
63 7 0.08
64 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (59 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
Found at i:48649 original size:23 final size:23
Alignment explanation
Indices: 48573--48650 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
48563 CCTTATGGAC
* *
48573 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTTCGGTGCA
* * *
48597 ATTCTACGCGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
48620 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
48643 ATTATATG
1 ATTATATG
48651 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 43 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTTCGGTGCA
Found at i:49739 original size:21 final size:21
Alignment explanation
Indices: 49702--49746 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
49692 GATTTCTGGG
*
49702 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
49723 CAAGGGGAA-CTGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
49744 CAA
1 CAA
49747 ACGGACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:51517 original size:103 final size:103
Alignment explanation
Indices: 51338--51541 Score: 381
Period size: 103 Copynumber: 2.0 Consensus size: 103
51328 GTCTACGCGG
51338 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
1 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
* *
51403 TTGGCATATGTATATGATTCTTAAGGAATGATATGTGT
66 CTAGCATATGTATATGATTCTTAAGGAATGATATGTGT
51441 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
1 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
*
51506 CTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CTAGCATATGTATATGATTCTTAAGGAATGATATGT
51542 AGTCCTTATG
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
CTAGCATATGTATATGATTCTTAAGGAATGATATGTGT
Found at i:51598 original size:23 final size:23
Alignment explanation
Indices: 51565--51627 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
51555 ATTATTATAT
51565 GGCACTACGGTGCAATTCTACGA
1 GGCACTACGGTGCAATTCTACGA
* *
51588 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGA
* *
51611 GGCACTTCGGTACAATT
1 GGCACTACGGTGCAATT
51628 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGA
Found at i:54691 original size:20 final size:21
Alignment explanation
Indices: 54656--54697 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
54646 CAACAAACTG
*
54656 AAATTTAATAAAATATAAATA
1 AAATTCAATAAAATATAAATA
54677 AAATTCAAT-AAATATAAATA
1 AAATTCAATAAAATATAAATA
54697 A
1 A
54698 CAATCCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTCAATAAAATATAAATA
Found at i:54889 original size:27 final size:26
Alignment explanation
Indices: 54852--54907 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
54842 ATCTATTATT
* *
54852 ATTAATCAACAAATTGTCTCGAACCC
1 ATTAATCAACAAACTGTCCCGAACCC
*
54878 ATTAATTCAACAAGCTGTCCCGAACCC
1 ATTAA-TCAACAAACTGTCCCGAACCC
54905 ATT
1 ATT
54908 CAACAAGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.36, C:0.29, G:0.09, T:0.27
Consensus pattern (26 bp):
ATTAATCAACAAACTGTCCCGAACCC
Found at i:60450 original size:17 final size:17
Alignment explanation
Indices: 60424--60457 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60414 GTATTAAAAA
* *
60424 TTATTGATAATATATTT
1 TTATTAATAAAATATTT
60441 TTATTAATAAAATATTT
1 TTATTAATAAAATATTT
60458 CATTTATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTATTAATAAAATATTT
Found at i:61154 original size:13 final size:12
Alignment explanation
Indices: 61136--61169 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
61126 AACAATTAAA
61136 TTTTAAAAATCAC
1 TTTTAAAAA-CAC
61149 TTTTAAACAACAC
1 TTTTAAA-AACAC
61162 TTTTAAAA
1 TTTTAAAA
61170 GTTTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 17 0.85
14 2 0.10
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTTAAAAACAC
Found at i:63189 original size:52 final size:49
Alignment explanation
Indices: 63108--63214 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 49
63098 TTTTTTTTAT
* *
63108 ATTAAAAACTCAATTTTTTAGTGGGAATGAATGAATTTGGTTTACTTGG
1 ATTAAAAACTCAATTTTTTAGTGGAAATGAATGAATTTGGTTTACTTAG
* *
63157 ATTAAGAAACTCAACTTTTTTAAGTGGAAATGAATGAATTTTGTTTATTTAG
1 ATTAA-AAACTCAA-TTTTTT-AGTGGAAATGAATGAATTTGGTTTACTTAG
63209 ATTAAA
1 ATTAAA
63215 CACTGAAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 5 0.10
50 8 0.16
51 7 0.14
52 31 0.61
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (49 bp):
ATTAAAAACTCAATTTTTTAGTGGAAATGAATGAATTTGGTTTACTTAG
Found at i:64580 original size:33 final size:33
Alignment explanation
Indices: 64538--64604 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
64528 ATGGAATTTT
64538 TCTGTTTATTTATTTGGCAGTGATGCTGTCTGG
1 TCTGTTTATTTATTTGGCAGTGATGCTGTCTGG
64571 TCTGTTTATTTATTTGGCAGTGATGCTGTCTGG
1 TCTGTTTATTTATTTGGCAGTGATGCTGTCTGG
64604 T
1 T
64605 ATGAGGCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.49
Consensus pattern (33 bp):
TCTGTTTATTTATTTGGCAGTGATGCTGTCTGG
Found at i:68695 original size:45 final size:45
Alignment explanation
Indices: 68631--68723 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
68621 TGCCAATCAA
68631 GGGTGGAAATTACAACAGTTTGACATTAAGAATGCCTACATGCAT
1 GGGTGGAAATTACAACAGTTTGACATTAAGAATGCCTACATGCAT
*
68676 GGGTGGAAATTACAACAGTTTGACATTAAGAATGCCTTCATGCAT
1 GGGTGGAAATTACAACAGTTTGACATTAAGAATGCCTACATGCAT
68721 GGG
1 GGG
68724 GATTGTCGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (45 bp):
GGGTGGAAATTACAACAGTTTGACATTAAGAATGCCTACATGCAT
Found at i:70055 original size:13 final size:13
Alignment explanation
Indices: 70037--70065 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
70027 GCACCGTACT
70037 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
70050 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
70063 CCG
1 CCG
70066 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:70354 original size:16 final size:16
Alignment explanation
Indices: 70333--70364 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
70323 CTTTCCTCTC
*
70333 TGTTTTTTTTTTCGTT
1 TGTTTTTTTTGTCGTT
70349 TGTTTTTTTTGTCGTT
1 TGTTTTTTTTGTCGTT
70365 CTCTGCCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (16 bp):
TGTTTTTTTTGTCGTT
Found at i:70766 original size:3 final size:3
Alignment explanation
Indices: 70758--70862 Score: 115
Period size: 3 Copynumber: 34.7 Consensus size: 3
70748 TTATTTATTA
*
70758 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * * *
70805 AAT -AT AAT TAT TAT AAT AAT AAA AAT ACT AAAT AAT AAT AAT -TT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
70849 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
70863 ATTTAAATGA
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
2 3 0.03
3 76 0.87
4 8 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:70837 original size:39 final size:39
Alignment explanation
Indices: 70756--70862 Score: 137
Period size: 39 Copynumber: 2.8 Consensus size: 39
70746 AATTATTTAT
* *
70756 TAAATAATAATAATAT-A-TAATATTAATAATAATAATAA
1 TAAATAATAATAATATAATTATTA-TAATAATAAAAATAA
*
70794 TAAATAATAATAATATAATTATTATAATAATAAAAATAC
1 TAAATAATAATAATATAATTATTATAATAATAAAAATAA
* * *
70833 TAAATAATAATAATTTAATAATAATAATAA
1 TAAATAATAATAATATAATTATTATAATAA
70863 ATTTAAATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 16 0.26
39 41 0.67
40 4 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (39 bp):
TAAATAATAATAATATAATTATTATAATAATAAAAATAA
Found at i:70863 original size:36 final size:36
Alignment explanation
Indices: 70757--70863 Score: 134
Period size: 33 Copynumber: 3.0 Consensus size: 36
70747 ATTATTTATT
70757 AAATAAT-AATAATATATAATATTAATAATAATAATAA
1 AAATAATAAATAATA-ATAAT-TTAATAATAATAATAA
*
70794 TAAATAAT-AATAAT-ATAA-TT-ATTATAATAATAA
1 -AAATAATAAATAATAATAATTTAATAATAATAATAA
*
70827 AAATACTAAATAATAATAATTTAATAATAATAATAA
1 AAATAATAAATAATAATAATTTAATAATAATAATAA
70863 A
1 A
70864 TTTAAATGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
32 6 0.10
33 18 0.29
34 6 0.10
35 2 0.03
36 17 0.27
38 13 0.21
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.36
Consensus pattern (36 bp):
AAATAATAAATAATAATAATTTAATAATAATAATAA
Found at i:71418 original size:223 final size:223
Alignment explanation
Indices: 70990--71576 Score: 1027
Period size: 223 Copynumber: 2.7 Consensus size: 223
70980 GGAAATGTTT
*
70990 GAAACA-CATGCACTGAAGGCTTAC--ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 GAAACATCATGCACTGAAGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
71052 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCGAAGGCTTTGAAAACATCAAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCGAAGGCTTTGAAAACATCAAA
71117 AAGCT-CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAGACCCGAAGGCTTTGA
131 AAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGAGACCCGAAGGCTTTGA
71181 AAACATCAAAAAGCTCCCG-AGGCTTTTTG
195 AAACATCAAAAAGCT-CCGAAGGCTTTTTG
71210 GAAACATCATGCACTGAAGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 GAAACATCATGCACTGAAGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
71275 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAA
71340 AAAGCTCCCGAAGGCTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
130 AAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGA-GACCCGAAGGCTTTG
71404 AAAACATC-AAAAGCTCCGAAGGCTTTTTG
194 AAAACATCAAAAAGCTCCGAAGGCTTTTTG
71433 GAAACATCATGCACTGAATGAC-TACAGATGACCCGAAGGC-TTGAAAACATC-AAAAGCTCCCG
1 GAAACATCATGCACTGAA-GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71495 AAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCGAAGG-TTTGAAAACATCAA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCGAAGGCTTTGAAAACATCAA
71558 AAAGCTCCCGAAGGCTTTT
130 AAAGCTCCCGAAGGCTTTT
71577 TGG
Statistics
Matches: 357, Mismatches: 2, Indels: 18
0.95 0.01 0.05
Matches are distributed among these distances:
218 33 0.09
219 7 0.02
220 43 0.12
221 33 0.09
222 14 0.04
223 159 0.45
224 60 0.17
225 8 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (223 bp):
GAAACATCATGCACTGAAGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCGAAGGCTTTGAAAACATCAAA
AAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGAGACCCGAAGGCTTTGAA
AACATCAAAAAGCTCCGAAGGCTTTTTG
Found at i:71462 original size:73 final size:76
Alignment explanation
Indices: 70990--71579 Score: 1029
Period size: 74 Copynumber: 8.0 Consensus size: 76
70980 GGAAATGTTT
70990 GAAACA-CATGCACTGAAGG-CTTAC--ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71051 AAGGCTTTTTG
66 AAGGCTTTTTG
*
71062 GAAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCT-CCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71125 AAGGCTTTTTG
66 AAGGCTTTTTG
71136 GAAACATCATGCACTGAAGGACTTACAGA-GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71200 -AGGCTTTTTG
66 AAGGCTTTTTG
71210 GAAACATCATGCACTGAA-GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71274 AAGGCTTTTTG
66 AAGGCTTTTTG
71285 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71350 AAGGC-TTTTG
66 AAGGCTTTTTG
71360 G-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT-CCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71422 AAGGCTTTTTG
66 AAGGCTTTTTG
*
71433 GAAACATCATGCACTGAATGAC-TACAGATGACCCGAAGGC-TTGAAAACATC-AAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71495 AAGGC-TTTTG
66 AAGGCTTTTTG
71505 GAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGG-TTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
71568 AAGGCTTTTTG
66 AAGGCTTTTTG
71579 G
1 G
Statistics
Matches: 499, Mismatches: 3, Indels: 30
0.94 0.01 0.06
Matches are distributed among these distances:
72 76 0.15
73 89 0.18
74 214 0.43
75 65 0.13
76 55 0.11
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Done.