Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001236.1 Hibiscus syriacus cultivar Beakdansim tig00002432_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: 73259
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:12942 original size:26 final size:26
Alignment explanation
Indices: 12899--12949 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12889 GTATTGGGAG
*
12899 AAAGCTAGAATGATTTAGGATGATTTT
1 AAAGCTAGAATGAGTTAGGAT-ATTTT
*
12926 AAAGCTA-AATGGGTTAGGATATTT
1 AAAGCTAGAATGAGTTAGGATATTT
12950 ATAGTTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 11 0.50
27 7 0.32
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (26 bp):
AAAGCTAGAATGAGTTAGGATATTTT
Found at i:15387 original size:28 final size:29
Alignment explanation
Indices: 15347--15409 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
15337 ATCCTAAAAG
*
15347 ATAAAAAATATAAAATAATTATATTTTTA
1 ATAAAAAATATAAAATAACTATATTTTTA
**
15376 ATAAAAAA-ATAATTTAACTATATTTTTA
1 ATAAAAAATATAAAATAACTATATTTTTA
*
15404 TTAAAA
1 ATAAAA
15410 TTAATCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAAAAATATAAAATAACTATATTTTTA
Found at i:25586 original size:7 final size:7
Alignment explanation
Indices: 25551--25582 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
25541 CTTCATAACC
25551 TTTCCAT
1 TTTCCAT
25558 TTTCCAT
1 TTTCCAT
25565 TTTCCAT
1 TTTCCAT
*
25572 TTTCAAT
1 TTTCCAT
25579 TTTC
1 TTTC
25583 AATTATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTCCAT
Found at i:37209 original size:21 final size:21
Alignment explanation
Indices: 37183--37237 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
37173 CAGTTTCCAG
37183 ATTCGCAACGCGATTTCCCAA
1 ATTCGCAACGCGATTTCCCAA
*** * **
37204 ATTCGCGTTGCGATTTTCCTG
1 ATTCGCAACGCGATTTCCCAA
37225 ATTCGCAACGCGA
1 ATTCGCAACGCGA
37238 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ATTCGCAACGCGATTTCCCAA
Found at i:37252 original size:20 final size:20
Alignment explanation
Indices: 37227--37274 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
37217 TTTTCCTGAT
37227 TCGCAACGCGAATAC-GTAAA
1 TCGCAACGCGAAT-CTGTAAA
*
37247 TCGCAATGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
37267 TCGCAACG
1 TCGCAACG
37275 AGATTCTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:37282 original size:20 final size:20
Alignment explanation
Indices: 37227--37282 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
37217 TTTTCCTGAT
*
37227 TCGCAACGCGAATAC-GTAAA
1 TCGCAACGAGAAT-CTGTAAA
* *
37247 TCGCAATGCGAATCTGTAAA
1 TCGCAACGAGAATCTGTAAA
*
37267 TCGCAACGAGATTCTG
1 TCGCAACGAGAATCTG
37283 ACTATCGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGAGAATCTGTAAA
Found at i:38157 original size:24 final size:24
Alignment explanation
Indices: 38130--38183 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
38120 GTATTCGAAA
38130 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
38154 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
38178 TTTGAT
1 TTTGAT
38184 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:40634 original size:20 final size:20
Alignment explanation
Indices: 40609--40697 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
40599 CAACGTGGAA
40609 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
40629 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
40649 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
40669 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
40689 ATCGCAACG
1 ATCGCAACG
40698 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:40757 original size:34 final size:33
Alignment explanation
Indices: 40669--40764 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
40659 GGAATTGACT
* **
40669 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
40703 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
40736 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
40765 CGAAATTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:40760 original size:20 final size:19
Alignment explanation
Indices: 40702--40770 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
40692 GCAACGAGAG
40702 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
40721 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
40735 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
40755 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
40771 TAGTTTTGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:40824 original size:34 final size:34
Alignment explanation
Indices: 40779--40874 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
40769 ATTAGTTTTG
*
40779 CGTTGCAATTTTCATTTTCGCATTGCGATTC-ACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTA-T
40813 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTAT
** * *
40846 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
40875 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTAT
Found at i:40995 original size:14 final size:14
Alignment explanation
Indices: 40976--41012 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40966 CATCAATTAA
40976 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
40990 ACAAATCATCTTTT
1 ACAAATCAACATTT
41004 ACAAATCAA
1 ACAAATCAA
41013 TTAAAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:42420 original size:21 final size:21
Alignment explanation
Indices: 42396--42472 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
42386 TTACAGTGGC
* *
42396 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGATGAGAGGGGA
* * *
42417 CTCTTGAGCGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGGA
* *
42438 CTCTTGAACGAT-AGGGGAGGC
1 CTCTTGAACGATGAGAGG-GGA
42459 CTCTTGAACGATGA
1 CTCTTGAACGATGA
42473 CAGGTGAGTC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.07
21 42 0.91
22 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGA
Found at i:42463 original size:42 final size:42
Alignment explanation
Indices: 42365--42472 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
42355 TTTAGAATGT
* * * * *
42365 TGGGAG-GGACATCTTCAACGATTACAGTGGCCTCTTGAACGG
1 TGGGAGAGGAC-TCTTGAACGATGATAGGGGCCTCTTGAACGA
* *
42407 TGGGAGGGGACTCTTGAGCGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
*
42449 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGACTCTTGAACGATGA
42473 CAGGTGAGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 48 0.87
43 7 0.13
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:42952 original size:20 final size:20
Alignment explanation
Indices: 42929--42998 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
42919 TGAAACTTAA
42929 AATCGCAACGCGAAAATGAC
1 AATCGCAACGCGAAAATGAC
* *
42949 AATCGCAATGCGAAAATAAC
1 AATCGCAACGCGAAAATGAC
* * **
42969 TATCGCAATGCGAATTTGAC
1 AATCGCAACGCGAAAATGAC
*
42989 TATCGCAACG
1 AATCGCAACG
42999 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAAAATGAC
Found at i:43068 original size:20 final size:20
Alignment explanation
Indices: 43040--43085 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
43030 CAACAAAATT
43040 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* **
43060 GCAATGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
43080 GCAACG
1 GCAACG
43086 AGAGAATCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:43158 original size:20 final size:20
Alignment explanation
Indices: 43130--43293 Score: 214
Period size: 20 Copynumber: 8.5 Consensus size: 20
43120 GATTCTCTCG
**
43130 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
43150 TTGCAATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
43170 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
43190 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
43210 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
43224 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
43244 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
43264 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
43284 TTGCGATAGT
1 TTGCGATAGT
43294 AAACTATTCT
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
14 7 0.05
16 6 0.05
18 6 0.05
20 110 0.85
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:43216 original size:94 final size:94
Alignment explanation
Indices: 43092--43293 Score: 307
Period size: 94 Copynumber: 2.2 Consensus size: 94
43082 AACGAGAGAA
* **
43092 TCGCAATGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAA
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAA
*
43156 TAGTCATTTTCGTATTGCGATAGTCATTT
66 TAGTCATTTTCGCATTGCGATAGTCATTT
* ** * *
43185 TCGTATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGA
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAA
*
43250 TAGTCATTTTCGCGTTGCGATAGTCATTT
66 TAGTCATTTTCGCATTGCGATAGTCATTT
43279 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
43294 AAACTATTCT
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 13 0.13
94 84 0.87
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (94 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAA
TAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:43233 original size:74 final size:74
Alignment explanation
Indices: 43150--43290 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 74
43140 CAAATTCGCA
* *
43150 TTGCAATAGTCATTTTCGTATTGCGATAGTCATTTTCGTATTGCGATAGTCATTTTCGCATTGCG
1 TTGCAATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
43215 ATTCTCTCG
66 ATTCTCTCG
* * *
43224 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCG
1 TTGCAATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
43289 AT
66 AT
43291 AGTAAACTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (74 bp):
TTGCAATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
ATTCTCTCG
Found at i:45211 original size:20 final size:20
Alignment explanation
Indices: 45168--45235 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
45158 GAAACTTTAA
* **
45168 ATCGCAACACGAAAAGGAAA
1 ATCGCAACACGAAAATGACT
45188 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
45208 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
45228 ATCGCAAC
1 ATCGCAAC
45236 GCAAGAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:45304 original size:20 final size:20
Alignment explanation
Indices: 45279--45327 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
45269 GCGATTCTCT
45279 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
45299 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
45319 CGTTGCGAT
1 CGTTGCGAT
45328 TCACTCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:45940 original size:20 final size:20
Alignment explanation
Indices: 45917--45969 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
45907 CGATAGTCAG
*
45917 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
45937 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
45957 ATTCGCATTGCGA
1 ATTCGCATTGCGA
45970 ATCAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:49270 original size:23 final size:22
Alignment explanation
Indices: 49244--49287 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
49234 TATAAAAAAT
49244 TATTTTTTATTAAATATTTTTAG
1 TATTTTTTATTAAAT-TTTTTAG
*
49267 TATTTTTTATTTAATTTTTTA
1 TATTTTTTATTAAATTTTTTA
49288 AATAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTAG
Found at i:54435 original size:87 final size:87
Alignment explanation
Indices: 54289--54451 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
54279 TATGTTATAT
* *
54289 TATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
54354 AGCGCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
* *
54376 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
54441 AACGCTTATAT
66 AACGCTTATAT
54452 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AACGCTTATATAATAAAATAGG
Found at i:54894 original size:182 final size:182
Alignment explanation
Indices: 54587--55247 Score: 1162
Period size: 182 Copynumber: 3.6 Consensus size: 182
54577 TGCGTTCACC
** *
54587 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
*
54652 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
54716 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
54769 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
*
54834 TTTATAAAGTATCGACATTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
54899 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
54951 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
*
55016 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
55081 TACTTATAATAAATTATCGACACTTTCAACATAACCGATAGCACTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
55133 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
* * *
55198 TTTATAAAGTATCGACACTTTATTGACGATATAACTTATTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
55248 AAAGGTAAAA
Statistics
Matches: 458, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
181 2 0.00
182 456 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:58135 original size:181 final size:180
Alignment explanation
Indices: 57814--58286 Score: 651
Period size: 181 Copynumber: 2.6 Consensus size: 180
57804 CGTACTTACG
* * *
57814 AAAGTATCGATACTTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATACC-ATTT
*
57879 TATCATATTTTTACATGTTATATCTTTGTTTGATCGATACATTTTTTAAAGTATCGACACTTTAT
65 TATCATATTTTTACATGTTATATCGTTG-TTGATCGATACATTTTTTAAAGTATCGACACTTTAT
* *
57944 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCGTTATA-T
129 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * * *
57995 AAAGTTTCGACACTTTCAATATATCCGGTAGCGTTTTAACGGTTTCATCATTTTGATACCATTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATACCA-TTT
* *
58060 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTAT
65 TATCATATTTTTACATGTTATATCGTTGTTGATCGATACATTTTTT-AAAGTATCGACACTTTAT
*
58125 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
129 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * ** **
58177 AAAGTACCGACACTTTAAATATATTCAGTACCACTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATAC-CATTT
* * * *
58242 TGTCATAGTTTTATATGTTATATCGTTGTGGATCGATACATTTTT
65 TATCATATTTTTACATGTTATATCGTTGTTGATCGATACATTTTT
58287 AATTTGGATC
Statistics
Matches: 255, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
180 18 0.07
181 147 0.58
182 90 0.35
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATACCATTTT
ATCATATTTTTACATGTTATATCGTTGTTGATCGATACATTTTTTAAAGTATCGACACTTTATAG
GCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
Found at i:61263 original size:16 final size:17
Alignment explanation
Indices: 61229--61265 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
61219 TAATTTTAAA
61229 AAATATATTTATATATT
1 AAATATATTTATATATT
61246 AAATAATATTT-T-TATT
1 AAAT-ATATTTATATATT
61262 AAAT
1 AAAT
61266 TATGAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATATATTTATATATT
Found at i:61447 original size:38 final size:39
Alignment explanation
Indices: 61366--61555 Score: 199
Period size: 38 Copynumber: 4.8 Consensus size: 39
61356 GCAAACGGTG
* **
61366 TTTGAAAATACATATATAATATATAGTCTTT-AAAAAAACATT
1 TTTG-AAA-ACATATATATTATATAGT-TTTGAAAATTA-ATT
* * *
61408 TTTGAAAACATATACATTATATAGTTTTTAAAA-CAATTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATTAA-TT
* *
61447 TTTG-AAATATATATATTATATAGTTTTGAAAATTAGTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATTAATT
* * *
61485 TTTTAAAATATATATATTATATAGTTTTGAAAATTAGTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATTAATT
*
61524 TTT-AAAAAATATATATTATATAGTTTTGAAAA
1 TTTGAAAACATATATATTATATAGTTTTGAAAA
61556 GAGAAAATCG
Statistics
Matches: 134, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
38 59 0.44
39 48 0.36
40 20 0.15
41 3 0.02
42 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
TTTGAAAACATATATATTATATAGTTTTGAAAATTAATT
Found at i:61487 original size:39 final size:39
Alignment explanation
Indices: 61406--61555 Score: 214
Period size: 38 Copynumber: 3.9 Consensus size: 39
61396 TAAAAAAACA
* * * * * *
61406 TTTTTGAAAACATATACATTATATAGTTTTTAAAA-CAA
1 TTTTTTAAAATATATATATTATATAGTTTTGAAAATTAG
*
61444 TTTTTTGAAATATATATATTATATAGTTTTGAAAATTAG
1 TTTTTTAAAATATATATATTATATAGTTTTGAAAATTAG
61483 TTTTTTAAAATATATATATTATATAGTTTTGAAAATTAG
1 TTTTTTAAAATATATATATTATATAGTTTTGAAAATTAG
*
61522 -TTTTTAAAAAATATATATTATATAGTTTTGAAAA
1 TTTTTTAAAATATATATATTATATAGTTTTGAAAA
61556 GAGAAAATCG
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 63 0.62
39 39 0.38
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (39 bp):
TTTTTTAAAATATATATATTATATAGTTTTGAAAATTAG
Found at i:61487 original size:77 final size:77
Alignment explanation
Indices: 61406--61555 Score: 219
Period size: 77 Copynumber: 1.9 Consensus size: 77
61396 TAAAAAAACA
* * * *
61406 TTTTTGAAAACATATACATTATATAGTTTTTAAAACAATTTTTTGAAATATATATATTATATAGT
1 TTTTTGAAAACATATACATTATATAGTTTTGAAAACAAGTTTTTAAAAAATATATATTATATAGT
61471 TTTGAAAATTAG
66 TTTGAAAATTAG
* * * **
61483 TTTTTTAAAATATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAATATATATTATATAGT
1 TTTTTGAAAACATATACATTATATAGTTTTGAAAACAAGTTTTTAAAAAATATATATTATATAGT
61548 TTTGAAAA
66 TTTGAAAA
61556 GAGAAAATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 64 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (77 bp):
TTTTTGAAAACATATACATTATATAGTTTTGAAAACAAGTTTTTAAAAAATATATATTATATAGT
TTTGAAAATTAG
Found at i:61730 original size:21 final size:21
Alignment explanation
Indices: 61701--61774 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
61691 GCGCTGCATT
61701 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
61722 TCGCATTGCGAT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
61742 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
61763 TCGCGTTACGAT
1 TCGCGTTGCGAT
61775 TTTCCTTTTC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:61750 original size:20 final size:20
Alignment explanation
Indices: 61722--61835 Score: 70
Period size: 20 Copynumber: 5.6 Consensus size: 20
61712 TAGTTGAAAA
*
61722 TCGCATTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCTATT
* ** **
61742 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCTATT
*
61763 TCGCGTTACGATTTTCCT-TT
1 TCGCGTTGCGATTTT-CTATT
** **
61783 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCTA-TT
*
61804 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCTATT
61824 TCGCGTTGCGAT
1 TCGCGTTGCGAT
61836 AGTGTACAGT
Statistics
Matches: 66, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
19 2 0.03
20 36 0.55
21 28 0.42
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCTATT
Found at i:61810 original size:21 final size:21
Alignment explanation
Indices: 61786--61857 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
61776 TTCCTTTTCG
61786 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
61807 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
*
61825 CGCGTTGCGATAGTGTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
61848 CGTTGCGATA
1 CGTTGCGATA
61858 ATTTTCTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.22
21 19 0.47
22 4 0.10
23 2 0.05
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:61856 original size:41 final size:41
Alignment explanation
Indices: 61697--61838 Score: 198
Period size: 41 Copynumber: 3.5 Consensus size: 41
61687 ATTCGCGCTG
*
61697 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
61738 TATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
61779 CTTTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
61820 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
61839 GTACAGTGTC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.01
41 88 0.98
42 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:61919 original size:6 final size:6
Alignment explanation
Indices: 61908--61940 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
61898 GACACGTATT
61908 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
61941 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:62456 original size:6 final size:6
Alignment explanation
Indices: 62435--62471 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
62425 TCTCGTCTCG
62435 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
62472 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:62814 original size:14 final size:13
Alignment explanation
Indices: 62786--62810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62776 ATATATTATA
62786 TAGTTTTTAAAAT
1 TAGTTTTTAAAAT
62799 TAGTTTTTAAAA
1 TAGTTTTTAAAA
62811 ATTATATATT
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:0.08, T:0.52
Consensus pattern (13 bp):
TAGTTTTTAAAAT
Found at i:62856 original size:39 final size:39
Alignment explanation
Indices: 62775--62960 Score: 225
Period size: 38 Copynumber: 4.8 Consensus size: 39
62765 AATATATATA
* * *
62775 TATATATTATATAGTTTTTAAAATTA-GTTTTTAAAAAT
1 TATATATTATATAGTTTTGAAAATTATTTTTTTAAAAAC
* *
62813 TATATATTATATAATTTTGAAAATTATTTTTTTCAAAAC
1 TATATATTATATAGTTTTGAAAATTATTTTTTTAAAAAC
* * * *
62852 TATATATTATGTGGTTTTGAAAGTTATTTTTTTTAAAA-
1 TATATATTATATAGTTTTGAAAATTATTTTTTTAAAAAC
*
62890 TATATATTATATGGTTTTGAAAATTATTTTCTTTAAAAAC
1 TATATATTATATAGTTTTGAAAATTATTTT-TTTAAAAAC
* *
62930 ATATATATTATATAG-TTTAAAAAATATTTTT
1 -TATATATTATATAGTTTTGAAAATTATTTTT
62961 CTTTATTTAT
Statistics
Matches: 128, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
38 52 0.41
39 50 0.39
40 13 0.10
41 13 0.10
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.52
Consensus pattern (39 bp):
TATATATTATATAGTTTTGAAAATTATTTTTTTAAAAAC
Found at i:62883 original size:77 final size:79
Alignment explanation
Indices: 62774--62947 Score: 237
Period size: 77 Copynumber: 2.2 Consensus size: 79
62764 AAATATATAT
*
62774 ATATATATTATATAGTTTTTAAAATTA-GTTTTTAAAAATTATATATTATATAATTTTGAAAATT
1 ATATATATTATATAGTTTTGAAAATTATGTTTTTAAAAA-TATATATTATATAATTTTGAAAATT
*
62838 ATTTT-TTTCAAAAC
65 ATTTTCTTTAAAAAC
* * * * * **
62852 -TATATATTATGTGGTTTTGAAAGTTATTTTTTTTAAAATATATATTATATGGTTTTGAAAATTA
1 ATATATATTATATAGTTTTGAAAATTATGTTTTTAAAAATATATATTATATAATTTTGAAAATTA
62916 TTTTCTTTAAAAAC
66 TTTTCTTTAAAAAC
62930 ATATATATTATATAGTTT
1 ATATATATTATATAGTTT
62948 AAAAAATATT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
77 50 0.61
78 17 0.21
79 15 0.18
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (79 bp):
ATATATATTATATAGTTTTGAAAATTATGTTTTTAAAAATATATATTATATAATTTTGAAAATTA
TTTTCTTTAAAAAC
Found at i:62977 original size:18 final size:19
Alignment explanation
Indices: 62954--62994 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
62944 GTTTAAAAAA
62954 TATTTTTCTTTATTT-ATT
1 TATTTTTCTTTATTTCATT
62972 TATTTTTCTTTATTTCATT
1 TATTTTTCTTTATTTCATT
62991 TATT
1 TATT
62995 ATTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTCTTTATTTCATT
Found at i:63993 original size:149 final size:149
Alignment explanation
Indices: 63723--64029 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
63713 CACCAAAGTG
*
63723 CCGCGTAGAATTGCACCGTAGTGCTATATAATAATGTCCATAAGGACCACATATTATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAG
63788 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
63853 ATACATATGTCCCTAAGGA
131 ATACATATGTCCCGAAGGA
63872 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAG
63937 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
64002 ATACATATGTCCCGAAGGA
131 ATACATATGTCCCGAAGGA
64021 CCGCGTAGA
1 CCGCGTAGA
64030 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 156 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAG
AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
ATACATATGTCCCGAAGGA
Found at i:65522 original size:21 final size:21
Alignment explanation
Indices: 65492--65536 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
65482 TTTTATTCGT
* *
65492 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
65513 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
65534 TTG
1 TTG
65537 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.