Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004501.1 Hibiscus syriacus cultivar Beakdansim tig00009929_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: 72186
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:215 original size:84 final size:83
Alignment explanation
Indices: 60--518 Score: 737
Period size: 84 Copynumber: 5.5 Consensus size: 83
50 CAAACCAATC
*
60 ATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA-TC-TTCTAAATTCAATGATTG
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-ATTCTTTC-AAATTCAATGATTG
123 GTTCTGTCCAACCAGATCAG
64 GTTCTGTCCAACCAGATCAG
*
143 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTTCAAATTCAATGATTAG
1 ATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTATTCTTTCAAATTCAATGATTGG
208 -TCTTGTCCAACCAGATCAG
65 TTC-TGTCCAACCAGATCAG
* * * * *
227 ATAACTCAAAGAACATTTCCAAAAGATGCTATTGAGCACATTACTCTTCCAAATTCAATGATTAG
1 ATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTATTCTTTCAAATTCAATGATTGG
292 -TCTTGTCCAACCAGATCAG
65 TTC-TGTCCAACCAGATCAG
* * *
311 ATAACTCAAAGAACATTTCCAAAAGATGCTATTAAGCACATTATTCTTTCAAATTCAATGATTGG
1 ATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTATTCTTTCAAATTCAATGATTGG
376 TTCTGTCCAACCAGATCAG
65 TTCTGTCCAACCAGATCAG
395 ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTTCAAATTCAATGATTGGT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTTCAAATTCAATGATTGGT
460 TCTGTCCAACCAGATCAG
66 TCTGTCCAACCAGATCAG
478 ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
519 CATTTGTTCC
Statistics
Matches: 358, Mismatches: 13, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
83 125 0.35
84 228 0.64
85 5 0.01
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (83 bp):
ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTTCAAATTCAATGATTGGT
TCTGTCCAACCAGATCAG
Found at i:1465 original size:8 final size:8
Alignment explanation
Indices: 1449--1526 Score: 88
Period size: 8 Copynumber: 9.6 Consensus size: 8
1439 CCTTTTTCCC
1449 CTTTTTTT
1 CTTTTTTT
*
1457 TTTTCTTTT
1 CTTT-TTTT
*
1466 TTTTTTTT
1 CTTTTTTT
1474 CTTTTTTT
1 CTTTTTTT
1482 -TTTTTTT
1 CTTTTTTT
1489 CTTTTTCTTT
1 C-TTTT-TTT
*
1499 CTTTCTTT
1 CTTTTTTT
1507 CTTTTTTT
1 CTTTTTTT
1515 C-TTTTTT
1 CTTTTTTT
1522 CTTTT
1 CTTTT
1527 CTCAGAATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
7 14 0.23
8 28 0.46
9 15 0.25
10 4 0.07
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
CTTTTTTT
Found at i:1508 original size:33 final size:34
Alignment explanation
Indices: 1449--1526 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 34
1439 CCTTTTTCCC
* *
1449 CTTTTTT-TTTTTCTTTTTTTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTCTTTTCTTTCTTTCTTTTTTT
*
1482 TTTTTTTCTTTTTC-TTTCTTTCTTTCTTTTTTT
1 CTTTTTTCTTTTTCTTTTCTTTCTTTCTTTTTTT
1515 CTTTTTTCTTTT
1 CTTTTTTCTTTT
1527 CTCAGAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 34 0.85
34 6 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (34 bp):
CTTTTTTCTTTTTCTTTTCTTTCTTTCTTTTTTT
Found at i:1538 original size:1 final size:1
Alignment explanation
Indices: 1450--1526 Score: 73
Period size: 1 Copynumber: 77.0 Consensus size: 1
1440 CTTTTTCCCC
* * * * * * *
1450 TTTTTTTTTTTCTTTTTTTTTTTTCTTTTTTTTTTTTTTCTTTTTCTTTCTTTCTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1515 CTTTTTTCTTTT
1 TTTTTTTTTTTT
1527 CTCAGAATTT
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:4995 original size:17 final size:18
Alignment explanation
Indices: 4970--5004 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4960 ATTTATGAAA
*
4970 TAAATAATGTAAA-AATG
1 TAAAAAATGTAAAGAATG
4987 TAAAAAATGTAAAGAATG
1 TAAAAAATGTAAAGAATG
5005 ATTGCCATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
TAAAAAATGTAAAGAATG
Found at i:12053 original size:15 final size:13
Alignment explanation
Indices: 12021--12058 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
12011 TTTGACAGAA
12021 AAAT-AAATAATG
1 AAATAAAATAATG
12033 AAATAAAATAATTG
1 AAATAAAATAA-TG
12047 CAAATAAAATAA
1 -AAATAAAATAA
12059 AACATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:13544 original size:45 final size:45
Alignment explanation
Indices: 13475--13566 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
13465 CCACCGTCTT
* *
13475 CGGTTGCCGGAAAAATTTTTTCTTTTATCTAAACGTAGATCGGAC
1 CGGTGGCCGGAAAAAATTTTTCTTTTATCTAAACGTAGATCGGAC
13520 CGGTGGCCGGAAAAAATTTTTCTTTTATCTAAACGTAGATCGGAC
1 CGGTGGCCGGAAAAAATTTTTCTTTTATCTAAACGTAGATCGGAC
13565 CG
1 CG
13567 TCCTAATGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (45 bp):
CGGTGGCCGGAAAAAATTTTTCTTTTATCTAAACGTAGATCGGAC
Found at i:14295 original size:3 final size:3
Alignment explanation
Indices: 14287--14375 Score: 160
Period size: 3 Copynumber: 29.7 Consensus size: 3
14277 AATATATATT
*
14287 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
14335 TAA TAA TAA TAA TAA TCA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14376 TGGGTAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16027 original size:18 final size:18
Alignment explanation
Indices: 16000--16034 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15990 AGATGATGAA
16000 TTTTAATAAAATATATTT
1 TTTTAATAAAATATATTT
* *
16018 TTTTATTAAAATTTATT
1 TTTTAATAAAATATATT
16035 ACATCAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATAAAATATATTT
Found at i:24016 original size:2 final size:2
Alignment explanation
Indices: 24009--24033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23999 GCACTTATGT
24009 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
24034 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:24038 original size:2 final size:2
Alignment explanation
Indices: 24033--24060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24023 TCTCTCTCTC
24033 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24061 AAGCCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25187 original size:32 final size:32
Alignment explanation
Indices: 25121--25188 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
25111 TAAAAGGTGA
* *
25121 ATTACAAACTTGTTATCATATATATAATGGTC
1 ATTACAAACTTGCTATCATATATATAATGATC
* * *
25153 ATTACAATCTTGCTATCATATATTTGATGATC
1 ATTACAAACTTGCTATCATATATATAATGATC
25185 ATTA
1 ATTA
25189 GTGAAAACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (32 bp):
ATTACAAACTTGCTATCATATATATAATGATC
Found at i:27190 original size:15 final size:14
Alignment explanation
Indices: 27144--27200 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 14
27134 ATTAATTTGT
27144 AATATTATAATATA
1 AATATTATAATATA
*
27158 AA-ATTA-AATGT-
1 AATATTATAATATA
*
27169 -ATATAAT-ATAT-
1 AATATTATAATATA
27180 AATATTATAATATA
1 AATATTATAATATA
27194 AATATTA
1 AATATTA
27201 GAAAGTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 10 0.29
13 8 0.24
14 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AATATTATAATATA
Found at i:30547 original size:200 final size:198
Alignment explanation
Indices: 30163--30834 Score: 843
Period size: 200 Copynumber: 3.4 Consensus size: 198
30153 GTAACATTAA
**
30163 AAATTTACCTATTACATTATAATTATCG-GTTTCGATATTTTTGGGATCGATACAATTT-TAAAT
1 AAATTTACCTATTACATTATAATTAT-GAGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
* * * * * * *
30226 GTATCGACACTTTATCCATGCACCTCGTTGGGCATTCATTCTGGA-AAAAAGTATCGACACAAAC
65 GTATCGACACTTTATGCGTGAACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACAC-AAG
* * * * * * * *
30290 TT-AAAAAGTGTCGATACATTATGTAGAACTATTTTATGATAAAACCGGTATATTTCTATCGGGT
129 TTCCACAAGTGTCGATACATTATATAGACCTATTTT-TTATAAAA-CTGTAAATTTCTATCGGTT
30354 ACATTGT
192 ACATTGT
* *
30361 AAATTTACCTATTACATTGTAATTATCG-GTTTCGATATTTTTGGGATCGATACTTTTAATAAAT
1 AAATTTACCTATTACATTATAATTAT-GAGTTTCGATATTTTTGGGATCGATACTTTTTATAAAT
* *
30425 GTATCGATACTTTATGCGTGAACCCCGTTTGGTATTCATTATGGACAAAAAGTATCGACACAAGT
65 GTATCGACACTTTATGCGTGAACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACACAAGT
30490 TCCACAAGTGTCGATACATTATATAGACCTATTTTTTCATAAAACATGTAAATTTCTATCGGTTA
130 TCCACAAGTGTCGATACATTATATAGACCTATTTTTT-ATAAAAC-TGTAAATTTCTATCGGTTA
*
30555 CATTAT
193 CATTGT
* * * * * *
30561 AAATTTACATATTATATTATAATTATGAGTTTCAATGTTTTTGGGATCTATACTTTTTATAAATA
1 AAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGGATCGATACTTTTTATAAATG
* * * * * * *
30626 TAACGACACTTTATGTGCGTA-CCCTTTTGAGCATTCATTTTGGACAACAAGTATCGACACAAGT
66 TATCGACACTTTATGCGTGAACCCCGTTTG-GCATTCATTATGGACAAAAAGTATCGACACAAGT
* *
30690 TCCACAAGTGTCGATACATTATATAGACCTATTTTCTTATAAAACTGGTAAATTTATATCAGTTA
130 TCCACAAGTGTCGATACATTATATAGACCTATTTT-TTATAAAACT-GTAAATTTCTATCGGTTA
30755 CATTGT
193 CATTGT
* * * *
30761 AAAATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGAGATCAATACTTTTTATAAATG
1 AAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGGATCGATACTTTTTATAAATG
30826 TATCGACAC
66 TATCGACAC
30835 ATATTTAGGT
Statistics
Matches: 415, Mismatches: 50, Indels: 16
0.86 0.10 0.03
Matches are distributed among these distances:
198 54 0.13
199 57 0.14
200 302 0.73
201 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGGATCGATACTTTTTATAAATG
TATCGACACTTTATGCGTGAACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACACAAGTT
CCACAAGTGTCGATACATTATATAGACCTATTTTTTATAAAACTGTAAATTTCTATCGGTTACAT
TGT
Found at i:32693 original size:20 final size:21
Alignment explanation
Indices: 32668--32706 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
32658 GTGGCTCTTT
*
32668 ACCGGTTTTGTCAT-TTTTAG
1 ACCGGTTTTATCATATTTTAG
32688 ACCGGTTTTATCATATTTT
1 ACCGGTTTTATCATATTTT
32707 TACCTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (21 bp):
ACCGGTTTTATCATATTTTAG
Found at i:33105 original size:182 final size:182
Alignment explanation
Indices: 32548--33104 Score: 855
Period size: 182 Copynumber: 3.1 Consensus size: 182
32538 CCTAAGTGTA
*
32548 GATACATTTTTATAAAGTATCAACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
1 GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
*
32613 AGTGTTGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTGGCTCTTTACCGGTTTTG
66 AGTGTTGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
*
32678 TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATTTTGTTATGGATC
131 TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATC
* * *
32730 GATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTTCAAA
1 GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
32795 AGTGTTGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
66 AGTGTTGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
* *
32860 TCATTTTTAGACCGGTTTTATTATATTTTTACATGTTATATTGTTATGGATC
131 TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATC
* * ** * *
32912 GATACATTTTTTTAAAGTATCGACATTTTATAAACGTTATTACTGCTTGTCTTTTAAATTCCAAA
1 GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
* * * * * * *
32977 AATGTCGATATTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTA
66 AGTGTTGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGC-TCTTTACCGGTTTT
* * * ** *
33041 GTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGATATAAATT
130 GTCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATC
33094 GATACATTTTT
1 GATACATTTTT
33105 TATTTGTATC
Statistics
Matches: 343, Mismatches: 31, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 342 1.00
183 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
AGTGTTGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATC
Found at i:39855 original size:20 final size:20
Alignment explanation
Indices: 39830--39868 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39820 CAAGTGGGAG
39830 ATTATTAGTTGTCATACAAA
1 ATTATTAGTTGTCATACAAA
39850 ATTATTAGTTGTCATACAA
1 ATTATTAGTTGTCATACAA
39869 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATACAAA
Found at i:39894 original size:21 final size:20
Alignment explanation
Indices: 39870--39911 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
39860 GTCATACAAC
*
39870 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
39891 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
39911 T
1 T
39912 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:46709 original size:48 final size:48
Alignment explanation
Indices: 46638--46782 Score: 281
Period size: 48 Copynumber: 3.0 Consensus size: 48
46628 TGTCTTACTT
46638 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
1 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
*
46686 TAGAGTGATCAGTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
1 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
46734 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
1 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
46782 T
1 T
46783 GGATGCTTCG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 95 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (48 bp):
TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
Found at i:47767 original size:23 final size:25
Alignment explanation
Indices: 47727--47774 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
47717 TTGTATTTCA
**
47727 AATGGTATAATGCTTGAC-TTTATT
1 AATGGTATAATGAATGACGTTTATT
47751 AATGGT-TAATGAATGACGTTTATT
1 AATGGTATAATGAATGACGTTTATT
47775 TCAACAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (25 bp):
AATGGTATAATGAATGACGTTTATT
Found at i:49481 original size:19 final size:19
Alignment explanation
Indices: 49454--49496 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
49444 TAGTATTGGT
* *
49454 TGGAATGGTTTAAACCGGC
1 TGGACTGGTCTAAACCGGC
49473 TGGACTGGTCTAAACCGGC
1 TGGACTGGTCTAAACCGGC
49492 TGGAC
1 TGGAC
49497 CGGACTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (19 bp):
TGGACTGGTCTAAACCGGC
Found at i:55348 original size:27 final size:27
Alignment explanation
Indices: 55310--55364 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
55300 TTGTTAGCCA
55310 GGTTACTTCAAGGCCTACTTAATTTAT
1 GGTTACTTCAAGGCCTACTTAATTTAT
55337 GGTTACTTCAAGGCCTACTTAATTTAT
1 GGTTACTTCAAGGCCTACTTAATTTAT
55364 G
1 G
55365 AATAAAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (27 bp):
GGTTACTTCAAGGCCTACTTAATTTAT
Found at i:58859 original size:17 final size:17
Alignment explanation
Indices: 58837--58902 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
58827 CAAAAGCAAA
58837 ATATAAATTCGTATTCG
1 ATATAAATTCGTATTCG
*
58854 ATAT-AATT--TAATC-
1 ATATAAATTCGTATTCG
* *
58867 ATATAAGATTCATATTCAA
1 ATATAA-ATTCGTATTC-G
*
58886 ATATAACTTCGTATTCG
1 ATATAAATTCGTATTCG
58903 TCGTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
13 4 0.11
14 5 0.13
15 3 0.08
16 4 0.11
17 8 0.21
18 8 0.21
19 6 0.16
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (17 bp):
ATATAAATTCGTATTCG
Found at i:64799 original size:31 final size:31
Alignment explanation
Indices: 64761--64824 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
64751 GAAACATAAA
**
64761 ATATGATCACTTTTGTTTTTAA-TTAATTAAG
1 ATATGATCAC-TTTCATTTTAATTTAATTAAG
64792 ATATGATCACTTTCATTTTAATTTAATTAAG
1 ATATGATCACTTTCATTTTAATTTAATTAAG
64823 AT
1 AT
64825 GTGCTCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (31 bp):
ATATGATCACTTTCATTTTAATTTAATTAAG
Found at i:65046 original size:24 final size:24
Alignment explanation
Indices: 65006--65062 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
64996 TAAAATTAAG
*
65006 TTAATAATAAAATATATTTAATAAA
1 TTAAT-ATAAAAAATATTTAATAAA
** *
65031 TTAATATAAAAAATATTTTTTAAG
1 TTAATATAAAAAATATTTAATAAA
65055 TTAATATA
1 TTAATATA
65063 TATATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TTAATATAAAAAATATTTAATAAA
Found at i:68411 original size:65 final size:63
Alignment explanation
Indices: 68290--68424 Score: 157
Period size: 65 Copynumber: 2.1 Consensus size: 63
68280 TTAAGATGTT
*
68290 CATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAAGGGAGTG
1 CATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAA--GAGTG
* * * * * *
68355 CATCGATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAATAGTG
1 CATCGATGCACTACC-CATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGAGTG
68418 CATCGAT
1 CATCGAT
68425 ACACATTGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
63 11 0.18
64 7 0.11
65 43 0.70
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (63 bp):
CATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGAGTG
Done.