Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003794.1 Hibiscus syriacus cultivar Beakdansim tig00008117_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: 105161
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:9904 original size:37 final size:38
Alignment explanation
Indices: 9827--9914 Score: 128
Period size: 37 Copynumber: 2.3 Consensus size: 38
9817 GACCTGACCT
*
9827 AAAAATATATACCTTCCACCCAAATTTGACGCGACTCG
1 AAAAATATATACCTTCCACCCAAATTTGACCCGACTCG
9865 AAAAATATATATCC-TCCACCC-AATTTGACCCGA-TCCG
1 AAAAATATATA-CCTTCCACCCAAATTTGACCCGACT-CG
9902 AAAAATATATACC
1 AAAAATATATACC
9915 CTTCACTCGA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
36 3 0.06
37 24 0.51
38 18 0.38
39 2 0.04
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (38 bp):
AAAAATATATACCTTCCACCCAAATTTGACCCGACTCG
Found at i:11371 original size:14 final size:14
Alignment explanation
Indices: 11354--11387 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11344 ACTGAAAACG
*
11354 TTTTTTAGAAAATA
1 TTTTTCAGAAAATA
*
11368 TTTTCCAGAAAATA
1 TTTTTCAGAAAATA
11382 TTTTTC
1 TTTTTC
11388 GTAAAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTTTCAGAAAATA
Found at i:11656 original size:31 final size:29
Alignment explanation
Indices: 11588--11657 Score: 70
Period size: 33 Copynumber: 2.2 Consensus size: 29
11578 AATATTATTT
*
11588 TTATAATTTTATAAATAAAAATATTAATAT
1 TTAT-ATTTTATAAATAAAAATATTAATAA
11618 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTA-T-AAATAAAAATATTAAT-AA
11651 TTATATT
1 TTATATT
11658 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 12 0.35
32 6 0.18
33 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (29 bp):
TTATATTTTATAAATAAAAATATTAATAA
Found at i:11936 original size:22 final size:23
Alignment explanation
Indices: 11906--11973 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
11896 ATTATTTTAT
* *
11906 TATAATATTAAAACTA-TAAT-AG
1 TATATTATTAAAA-TATTAATAAA
11928 TATATTATTAGAAATATTAATAAA
1 TATATTATTA-AAATATTAATAAA
*
11952 TATATT-TTAAATATTTTAATAA
1 TATATTATTAAA-ATATTAATAA
11974 TTAATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 13 0.33
23 19 0.49
24 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (23 bp):
TATATTATTAAAATATTAATAAA
Found at i:18125 original size:12 final size:12
Alignment explanation
Indices: 18108--18133 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18098 TAGTAACATA
18108 CATCGCATTGTT
1 CATCGCATTGTT
18120 CATCGCATTGTT
1 CATCGCATTGTT
18132 CA
1 CA
18134 ACTTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.38
Consensus pattern (12 bp):
CATCGCATTGTT
Found at i:18380 original size:2 final size:2
Alignment explanation
Indices: 18373--18455 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
18363 ATATGTGTAC
*
18373 AT AT AT AT AT AT AC AT 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 AT AT AT AT AT AT AT AT
18415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18456 CGAATATACA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19549 original size:3 final size:3
Alignment explanation
Indices: 19541--19579 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
19531 CAAAAATGAT
19541 TAA TAA TAA TAA TAA -ACA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TA
19580 GTTTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 28 0.85
4 4 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:21000 original size:22 final size:22
Alignment explanation
Indices: 20976--21017 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20966 TTTATTTAAT
20976 TTTTTCTT-TTTTTCCATTTTC
1 TTTTTCTTCTTTTTCCATTTTC
*
20997 TTTTTCTTCTTTTTTCATTTT
1 TTTTTCTTCTTTTTCCATTTT
21018 TCCATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTCTTTTTCCATTTTC
Found at i:21010 original size:15 final size:15
Alignment explanation
Indices: 20976--21018 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
20966 TTTATTTAAT
20976 TTTTTCTTTTTTTCC
1 TTTTTCTTTTTTTCC
* *
20991 ATTTTCTTTTTCTTCT
1 TTTTTCTTTTT-TTCC
21007 TTTTTCATTTTT
1 TTTTTC-TTTTT
21019 CCATCATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTTTCC
Found at i:22849 original size:23 final size:23
Alignment explanation
Indices: 22819--22865 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
22809 TAACAAATAT
22819 ACTCATCAAGTCCTCATTCGGAA
1 ACTCATCAAGTCCTCATTCGGAA
22842 ACTCATCAAGTCCTCATTCGGAA
1 ACTCATCAAGTCCTCATTCGGAA
22865 A
1 A
22866 ATCAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (23 bp):
ACTCATCAAGTCCTCATTCGGAA
Found at i:30486 original size:21 final size:21
Alignment explanation
Indices: 30460--30506 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
30450 AAATTGGTAT
30460 TCCTCGAGGGTTGGAGTCATA
1 TCCTCGAGGGTTGGAGTCATA
*
30481 TCCTCGAGGGTTGGAGTCATG
1 TCCTCGAGGGTTGGAGTCATA
30502 TCCTC
1 TCCTC
30507 TCGGTTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.32, T:0.30
Consensus pattern (21 bp):
TCCTCGAGGGTTGGAGTCATA
Found at i:31643 original size:8 final size:9
Alignment explanation
Indices: 31621--31650 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
31611 AAAAACAGGG
31621 AAAATAAAAT
1 AAAA-AAAAT
31631 AAAAAAAAT
1 AAAAAAAAT
31640 AAAAAAAAT
1 AAAAAAAAT
31649 AA
1 AA
31651 CACCCAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:32455 original size:12 final size:12
Alignment explanation
Indices: 32438--32463 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32428 TAGTAACATA
32438 CATCGCATTGTT
1 CATCGCATTGTT
32450 CATCGCATTGTT
1 CATCGCATTGTT
32462 CA
1 CA
32464 ACTTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.38
Consensus pattern (12 bp):
CATCGCATTGTT
Found at i:33817 original size:3 final size:3
Alignment explanation
Indices: 33809--33847 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
33799 CAAAAATGAT
33809 TAA TAA TAA TAA TAA -ACA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TA
33848 GTTTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 28 0.85
4 4 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:34727 original size:22 final size:24
Alignment explanation
Indices: 34684--34727 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
34674 AACTTAATTG
*
34684 TTTTATTTAATTATTTTTAAAAGA
1 TTTTATTTAATTATATTTAAAAGA
34708 TTTTA-TTAA-TATATTTAAAA
1 TTTTATTTAATTATATTTAAAA
34728 AAATTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTATTTAATTATATTTAAAAGA
Found at i:34729 original size:24 final size:24
Alignment explanation
Indices: 34684--34729 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
34674 AACTTAATTG
**
34684 TTTTATTTAATTATTTTTAAAAGA
1 TTTTATTTAATTATTTAAAAAAGA
34708 TTTTA-TTAATATATTTAAAAAA
1 TTTTATTTAAT-TATTTAAAAAA
34730 ATTATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTATTTAATTATTTAAAAAAGA
Found at i:36433 original size:14 final size:14
Alignment explanation
Indices: 36414--36446 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
36404 AGCCTCAACC
36414 GAGCCGGTTTTATG
1 GAGCCGGTTTTATG
36428 GAGCCGGTTTTATG
1 GAGCCGGTTTTATG
36442 GAGCC
1 GAGCC
36447 ACGATGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.36, T:0.30
Consensus pattern (14 bp):
GAGCCGGTTTTATG
Found at i:38312 original size:76 final size:76
Alignment explanation
Indices: 38168--38351 Score: 298
Period size: 76 Copynumber: 2.4 Consensus size: 76
38158 CTTAACCGGT
* * * * * *
38168 TAAAATAAAATAGACGCTACCTATTATGTT-AAACTACCTACTGGTTTGTTTGAATGTTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAATGTTACTAAT
38232 AATGTAAACGG
66 AATGTAAACGG
38243 TAAAATAAAATAGGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAATGTTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAATGTTACTAAT
38308 AATGTAAACGG
66 AATGTAAACGG
*
38319 TAAAATAAAGTAGGCGCTACCTATTACGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
38352 TAAGCGTTAC
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 28 0.28
76 73 0.72
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (76 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAATGTTACTAAT
AATGTAAACGG
Found at i:38440 original size:75 final size:75
Alignment explanation
Indices: 38349--38524 Score: 264
Period size: 75 Copynumber: 2.3 Consensus size: 75
38339 CTATTACGTT
* * * *
38349 AAATAAGCGTTACCTATTATGTTAAACTACCTACC-GATTTGTTTGAAGGTTACTAATAATGTAA
1 AAATAGGCGCTACCTATTATGTTAAAATACCTACCAG-TTTGTTTAAAGGTTACTAATAATGTAA
38413 ACGGTAAAATA
65 ACGGTAAAATA
* *
38424 AAATAGGCGCTACCTATTGTGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAA
1 AAATAGGCGCTACCTATTATGTTAAAATACCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAA
38489 CGGTAAAATA
66 CGGTAAAATA
* *
38499 AAATAGGCACTACCTATTTTGTTAAA
1 AAATAGGCGCTACCTATTATGTTAAA
38525 TAGGCGCTAC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 91 0.99
76 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (75 bp):
AAATAGGCGCTACCTATTATGTTAAAATACCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAA
CGGTAAAATA
Found at i:38449 original size:98 final size:99
Alignment explanation
Indices: 38250--38441 Score: 314
Period size: 98 Copynumber: 1.9 Consensus size: 99
38240 CGGTAAAATA
* *
38250 AAATAGGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAATGTTACTAATAATGTAA
1 AAATAAGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAAGGTTACTAATAATGTAA
*
38315 ACGGTAAAATAAAGTAGGCGCTACCTATTACGTT
66 ACGGTAAAATAAAATAGGCGCTACCTATTACGTT
* * * *
38349 AAATAAGCGTTACCTATTATGTT-AAACTACCTACCGATTTGTTTGAAGGTTACTAATAATGTAA
1 AAATAAGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAAGGTTACTAATAATGTAA
38413 ACGGTAAAATAAAATAGGCGCTACCTATT
66 ACGGTAAAATAAAATAGGCGCTACCTATT
38442 GTGTTAAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
98 66 0.77
99 20 0.23
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (99 bp):
AAATAAGCGCTACCTATTACGTTAAAAATACCTACCGATTTGTTTAAAGGTTACTAATAATGTAA
ACGGTAAAATAAAATAGGCGCTACCTATTACGTT
Found at i:38528 original size:23 final size:23
Alignment explanation
Indices: 38499--38570 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
38489 CGGTAAAATA
* *
38499 AAATAGGCACTACCTATTTTGTT
1 AAATAGGCGCTACCTATTATGTT
*
38522 AAATAGGCGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTATGTT
* *
38545 AAATAAGTGCTACCTATTATGTT
1 AAATAGGCGCTACCTATTATGTT
38568 AAA
1 AAA
38571 CTATCTACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTATGTT
Found at i:40127 original size:22 final size:22
Alignment explanation
Indices: 40097--40152 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
40087 TACGCGGTTT
*
40097 TTCGAGACAAATACATAGGTAC
1 TTCGGGACAAATACATAGGTAC
*
40119 TTCGGGACAAATACATAGGTCC
1 TTCGGGACAAATACATAGGTAC
40141 TTCGGGACAAAT
1 TTCGGGACAAAT
40153 TTCATATGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (22 bp):
TTCGGGACAAATACATAGGTAC
Found at i:40919 original size:20 final size:21
Alignment explanation
Indices: 40890--40931 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40880 ATGAAAGTTA
* *
40890 CTGTAGCA-GGGTATCGGTAC
1 CTGTAACAGGGGTATCGATAC
40910 CTGTAACAGGGGTATCGATAC
1 CTGTAACAGGGGTATCGATAC
40931 C
1 C
40932 CTTGAAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (21 bp):
CTGTAACAGGGGTATCGATAC
Found at i:42012 original size:73 final size:74
Alignment explanation
Indices: 41887--42036 Score: 275
Period size: 73 Copynumber: 2.0 Consensus size: 74
41877 GGTTGGGGTG
41887 TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGG
1 TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGG
*
41952 TGCTACCTA
66 CGCTACCTA
*
41961 TTACA-TTAATACCTATCGGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGG
1 TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGG
42025 CGCTACCTA
66 CGCTACCTA
42034 TTA
1 TTA
42037 TGTTATTATG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 69 0.93
74 5 0.07
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (74 bp):
TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGG
CGCTACCTA
Found at i:42344 original size:9 final size:9
Alignment explanation
Indices: 42330--42354 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42320 CATAGTAAAG
42330 AATTTAATA
1 AATTTAATA
42339 AATTTAATA
1 AATTTAATA
42348 AATTTAA
1 AATTTAA
42355 CTTTTTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTTAATA
Found at i:42540 original size:12 final size:12
Alignment explanation
Indices: 42523--42563 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
42513 ATGAGAGTAG
42523 TGTTCATGGTAC
1 TGTTCATGGTAC
*
42535 TGTTCAT--TAT
1 TGTTCATGGTAC
*
42545 TGTTCACGGTAC
1 TGTTCATGGTAC
42557 TGTTCAT
1 TGTTCAT
42564 ATCGTATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:46405 original size:22 final size:22
Alignment explanation
Indices: 46377--46424 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
46367 GGCAAATATG
46377 TCATTACTGTTCACGGTATTGT
1 TCATTACTGTTCACGGTATTGT
46399 TCATTACTGTTCACGGTATTGT
1 TCATTACTGTTCACGGTATTGT
46421 TCAT
1 TCAT
46425 ACCGTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (22 bp):
TCATTACTGTTCACGGTATTGT
Found at i:46442 original size:19 final size:19
Alignment explanation
Indices: 46418--46463 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
46408 TTCACGGTAT
*
46418 TGTTCATACCGTATAGTAC
1 TGTTCATACCATATAGTAC
* *
46437 TGTTCATACCATTTAGTAT
1 TGTTCATACCATATAGTAC
46456 TGTTCATA
1 TGTTCATA
46464 AATACGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTTCATACCATATAGTAC
Found at i:46756 original size:73 final size:74
Alignment explanation
Indices: 46628--46777 Score: 275
Period size: 73 Copynumber: 2.0 Consensus size: 74
46618 GGTTGGGGTG
*
46628 TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAATAGG
1 TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGATAAAATAAAATAGG
46693 CGCTACCTA
66 CGCTACCTA
*
46702 TTACA-TTAATACCTACTGGTTTGTTTAAAGATTACTAATAATGTAAACGATAAAATAAAATAGG
1 TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGATAAAATAAAATAGG
46766 CGCTACCTA
66 CGCTACCTA
46775 TTA
1 TTA
46778 TGTTATTATG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 69 0.93
74 5 0.07
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (74 bp):
TTACATTTAATACCTACCGGTTTGTTTAAAGATTACTAATAATGTAAACGATAAAATAAAATAGG
CGCTACCTA
Found at i:48274 original size:11 final size:12
Alignment explanation
Indices: 48258--48296 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
48248 GACTAAAATG
48258 AAAATAATAA-T
1 AAAATAATAATT
48269 AAAATAATAATT
1 AAAATAATAATT
*
48281 AAATTAATAACTT
1 AAAATAATAA-TT
48294 AAA
1 AAA
48297 CATATTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 10 0.40
13 5 0.20
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:51764 original size:6 final size:6
Alignment explanation
Indices: 51753--51807 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
51743 GACACGTATT
* *
51753 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
51801 ACCACG A
1 ACCACG A
51808 GCCGAGCCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:51815 original size:5 final size:5
Alignment explanation
Indices: 51805--51853 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
51795 ACCACGACCA
* * * *
51805 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
51854 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:57217 original size:57 final size:57
Alignment explanation
Indices: 57129--57242 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
57119 GGAGTGGACT
57129 GCTGGTGGTATTGCACTTCTGATCGGAAAGCACTCAGAGAGAACTCACAGAGAGAAC
1 GCTGGTGGTATTGCACTTCTGATCGGAAAGCACTCAGAGAGAACTCACAGAGAGAAC
57186 GCTGGTGGTATTGCACTTCTGATCGGAAAGCACTCAGAGAGAACTCACAGAGAGAAC
1 GCTGGTGGTATTGCACTTCTGATCGGAAAGCACTCAGAGAGAACTCACAGAGAGAAC
57243 TTTAGAAAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (57 bp):
GCTGGTGGTATTGCACTTCTGATCGGAAAGCACTCAGAGAGAACTCACAGAGAGAAC
Found at i:57786 original size:6 final size:6
Alignment explanation
Indices: 57775--57829 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
57765 GACACGTATT
* *
57775 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
57823 ACCACG A
1 ACCACG A
57830 GCCGAGCCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:57837 original size:5 final size:5
Alignment explanation
Indices: 57827--57885 Score: 82
Period size: 5 Copynumber: 11.8 Consensus size: 5
57817 ACCACGACCA
* * *
57827 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
*
57877 CGAGA CGAG
1 CGAGC CGAG
57886 ACGGACGGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:63989 original size:6 final size:6
Alignment explanation
Indices: 63978--64007 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
63968 CGAAGACACG
63978 TATTAC TATTAC TATTAC TATTAC TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC
64008 CACGACCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAC
Found at i:64015 original size:6 final size:6
Alignment explanation
Indices: 64006--64096 Score: 173
Period size: 6 Copynumber: 15.2 Consensus size: 6
63996 TATTACTATT
64006 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
64054 ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
64097 GCCGTGCCGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:75028 original size:17 final size:18
Alignment explanation
Indices: 74994--75028 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
74984 AATTTAAAGT
74994 AAAACAATTATATCTATAA
1 AAAACAATTATA-CTATAA
75013 AAAACAATTATA-TATA
1 AAAACAATTATACTATA
75029 TCATATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAACAATTATACTATAA
Found at i:77836 original size:19 final size:19
Alignment explanation
Indices: 77812--77852 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
77802 GTATGCTAGT
77812 GTGGTTTCAATTGTTTAAC
1 GTGGTTTCAATTGTTTAAC
*
77831 GTGGTTTCAGTTGTTTAAC
1 GTGGTTTCAATTGTTTAAC
77850 GTG
1 GTG
77853 CCTTTGGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.10, G:0.27, T:0.46
Consensus pattern (19 bp):
GTGGTTTCAATTGTTTAAC
Found at i:77955 original size:25 final size:25
Alignment explanation
Indices: 77927--77975 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
77917 TAATGGACTC
77927 GATTACAGCCTCTCGAGAGAGGCTT
1 GATTACAGCCTCTCGAGAGAGGCTT
77952 GATTACAGCCTCTCGAGAGAGGCT
1 GATTACAGCCTCTCGAGAGAGGCT
77976 CGAGTACGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (25 bp):
GATTACAGCCTCTCGAGAGAGGCTT
Found at i:83124 original size:65 final size:65
Alignment explanation
Indices: 83054--83184 Score: 201
Period size: 65 Copynumber: 2.0 Consensus size: 65
83044 TCCCTAATTT
* * *
83054 AATATTCTTCAATTATTCCTTTTTTATACCATACCTACAATTCACTTCATTCAAATTCAAA-AAG
1 AATATTCTTCAATTATTCATTTTTTATACCATACCTACAATTCAATTCACTCAAATT-AAAGAAG
83118 A
65 A
* *
83119 AATATTCTTCAATTATTCATTTTTTATACCATACTTATAATTCAATTCACTCAAATTAAAGAAGA
1 AATATTCTTCAATTATTCATTTTTTATACCATACCTACAATTCAATTCACTCAAATTAAAGAAGA
83184 A
1 A
83185 GAAGAACGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 3 0.05
65 57 0.95
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.40
Consensus pattern (65 bp):
AATATTCTTCAATTATTCATTTTTTATACCATACCTACAATTCAATTCACTCAAATTAAAGAAGA
Found at i:83645 original size:15 final size:15
Alignment explanation
Indices: 83627--83665 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
83617 TGTTAAGCAT
*
83627 GTTGATGTTGATAAC
1 GTTGATATTGATAAC
*
83642 GTTGATATTGATAAT
1 GTTGATATTGATAAC
*
83657 GTTAATATT
1 GTTGATATT
83666 TTTGATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (15 bp):
GTTGATATTGATAAC
Found at i:85354 original size:61 final size:61
Alignment explanation
Indices: 85286--85407 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
85276 CAACCAAAAC
* * *
85286 TCCCATATTTTACAACCGATAGAATATCTAAAAAGTTGTAAATGAAAGTTTTCGTTTTAGG
1 TCCCATATTTTACAACCGATAGAACATCTAAAAAATTGTAAATGAAAATTTTCGTTTTAGG
85347 TCCCATATTTTACAACCGATAGAACATCTAAAAAATTGTAAATGAAAATTTTCGTTTTAGG
1 TCCCATATTTTACAACCGATAGAACATCTAAAAAATTGTAAATGAAAATTTTCGTTTTAGG
85408 GTTTTTAGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (61 bp):
TCCCATATTTTACAACCGATAGAACATCTAAAAAATTGTAAATGAAAATTTTCGTTTTAGG
Found at i:88273 original size:65 final size:65
Alignment explanation
Indices: 88113--88273 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
88103 TTGTTTAAGG
* * * **
88113 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
88176 A
65 A
*
88177 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
88241 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
88274 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:89867 original size:147 final size:147
Alignment explanation
Indices: 89598--90026 Score: 785
Period size: 147 Copynumber: 2.9 Consensus size: 147
89588 GAGTCGAGGG
*
89598 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTATAAGACACA
1 TTCTACGCGGTCCTTCGGG--ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
89663 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATT
64 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
89728 ATATGGCACTACGGTGCAA
129 ATATGGCACTACGGTGCAA
89747 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
89812 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
89877 ATGGCACTACGGTGCAA
131 ATGGCACTACGGTGCAA
89894 TTCTACGCGGTCCTTCGGGATATATATA-TC--TGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
*
89956 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATT-TTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
90020 ATGGCAC
131 ATGGCAC
90027 ACGCAATTCT
Statistics
Matches: 277, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
143 11 0.04
144 91 0.33
146 2 0.01
147 154 0.56
149 19 0.07
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (147 bp):
TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAA
Found at i:91647 original size:2 final size:2
Alignment explanation
Indices: 91640--91665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
91630 ATCAGAAACA
91640 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
91666 TTAATCATTG
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:102121 original size:6 final size:6
Alignment explanation
Indices: 102110--102141 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
102100 TGAAGCTCTG
102110 CTTCCT CTTCCT CTTCCT CTTCCT -TTCC- CTTC
1 CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT CTTC
102142 TGTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 7 0.28
6 18 0.72
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCCT
Found at i:103124 original size:20 final size:20
Alignment explanation
Indices: 103095--103136 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
103085 TTCATCACAC
* *
103095 CAAATCCTCTCAACTTCTCT
1 CAAATACTCTCAAATTCTCT
*
103115 CAAATACTCTTAAATTCTCT
1 CAAATACTCTCAAATTCTCT
103135 CA
1 CA
103137 TAGCTCTTTA
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:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAATACTCTCAAATTCTCT
Done.