Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000721.1 Hibiscus syriacus cultivar Beakdansim tig00001399_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: 67105
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:568 original size:18 final size:18
Alignment explanation
Indices: 516--577 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
506 CCGTTAGACA
516 TGGGGAATCGGTACCCCC
1 TGGGGAATCGGTACCCCC
*
534 TGGGGGGAAT--GT-TCCCC
1 T--GGGGAATCGGTACCCCC
551 TGGGGAATCGGTACCCCC
1 TGGGGAATCGGTACCCCC
*
569 TGGGCAATC
1 TGGGGAATC
578 TGATTTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 7 0.19
17 7 0.19
18 15 0.42
20 7 0.19
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.19
Consensus pattern (18 bp):
TGGGGAATCGGTACCCCC
Found at i:21264 original size:21 final size:21
Alignment explanation
Indices: 21222--21264 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21212 TTTCTGGGCT
* *
21222 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
21243 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
21264 A
1 A
21265 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:21655 original size:14 final size:15
Alignment explanation
Indices: 21620--21659 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
21610 ATTATGAGAC
21620 ATGACATGAATTCAT
1 ATGACATGAATTCAT
* *
21635 ATAACATGCATT-AT
1 ATGACATGAATTCAT
21649 ATGACATGAAT
1 ATGACATGAAT
21660 ATGCAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGACATGAATTCAT
Found at i:21830 original size:25 final size:25
Alignment explanation
Indices: 21796--21862 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
21786 GTAGAGGGTA
21796 TACGCGGTCCTTCGGGACAATATTC
1 TACGCGGTCCTTCGGGACAATATTC
*
21821 TACGCGGTCCTTTGGGACAATATTC
1 TACGCGGTCCTTCGGGACAATATTC
21846 TACGCGGTCCTTCGGGA
1 TACGCGGTCCTTCGGGA
21863 TATATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (25 bp):
TACGCGGTCCTTCGGGACAATATTC
Found at i:22023 original size:23 final size:23
Alignment explanation
Indices: 21979--22023 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21969 ATTATTATAT
*
21979 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
22002 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
22024 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:28088 original size:21 final size:21
Alignment explanation
Indices: 28046--28088 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28036 TTTCTGGGCT
* *
28046 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
28067 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
28088 A
1 A
28089 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:28480 original size:14 final size:15
Alignment explanation
Indices: 28445--28484 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
28435 ATTATGAGAC
28445 ATGACATGAATTCAT
1 ATGACATGAATTCAT
* *
28460 ATAACATGCATT-AT
1 ATGACATGAATTCAT
28474 ATGACATGAAT
1 ATGACATGAAT
28485 ATGCAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGACATGAATTCAT
Found at i:28653 original size:25 final size:25
Alignment explanation
Indices: 28619--28694 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
28609 GGGTAGAGGG
28619 TCTACGCGGTCCTTCGGGATAATAT
1 TCTACGCGGTCCTTCGGGATAATAT
* *
28644 TCTACGCGGTCCTTTGGGACAATAT
1 TCTACGCGGTCCTTCGGGATAATAT
28669 TCTACGCGGTCCTTCGGGATATATAT
1 TCTACGCGGTCCTTCGGGATA-ATAT
28695 ATATTCTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 42 0.91
26 4 0.09
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGATAATAT
Found at i:28846 original size:23 final size:23
Alignment explanation
Indices: 28802--28846 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28792 ATTATTATAT
*
28802 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
28825 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
28847 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:30311 original size:13 final size:13
Alignment explanation
Indices: 30291--30328 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
30281 CAACCACACC
30291 TGACCCGACCCGT
1 TGACCCGACCCGT
*
30304 TTACCCGACCCGT
1 TGACCCGACCCGT
*
30317 TGACCTGACCCG
1 TGACCCGACCCG
30329 ACCTGTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.45, G:0.21, T:0.18
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:30327 original size:18 final size:18
Alignment explanation
Indices: 30288--30339 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
30278 TCACAACCAC
30288 ACCTGACCCGACCCGTT-
1 ACCTGACCCGACCCGTTG
30305 ---T-ACCCGACCCGTTG
1 ACCTGACCCGACCCGTTG
*
30319 ACCTGACCCGACCTGTTG
1 ACCTGACCCGACCCGTTG
30337 ACC
1 ACC
30340 CGTTGACCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 12 0.41
14 1 0.03
17 1 0.03
18 15 0.52
ACGTcount: A:0.17, C:0.44, G:0.19, T:0.19
Consensus pattern (18 bp):
ACCTGACCCGACCCGTTG
Found at i:31690 original size:18 final size:18
Alignment explanation
Indices: 31664--31698 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31654 TCAAAAGAAC
*
31664 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
31682 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
31699 CCAGATGGCA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:32834 original size:12 final size:12
Alignment explanation
Indices: 32819--32887 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
32809 GATACGTTAC
*
32819 CTGAATTATGTT
1 CTGAATTCTGTT
*
32831 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
32842 CTGGATTCTGTT
1 CTGAATTCTGTT
*
32854 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
*
32866 ATGAATTCTGTT
1 CTGAATTCTGTT
* *
32878 TTGATTTCTG
1 CTGAATTCTG
32888 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
11 11 0.24
12 33 0.72
13 2 0.04
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:32871 original size:47 final size:47
Alignment explanation
Indices: 32785--32889 Score: 117
Period size: 47 Copynumber: 2.2 Consensus size: 47
32775 TATTTTATCC
* *
32785 GATTTCTGAAT-TGAATTCTGTTCTGATACGTTACCTGAATTATGTTCT
1 GATTTCTG-ATCTGGATTCTGTTCTGATACGATA-CTGAATTATGTTCT
* *
32833 GA-TTCTGATCTGGATTCTGTTCTGATATCTGATA-TGAATTCTGTTTT
1 GATTTCTGATCTGGATTCTGTTCTGATA-C-GATACTGAATTATGTTCT
32880 GATTTCTGAT
1 GATTTCTGAT
32890 ATCTCCGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
46 2 0.04
47 34 0.69
48 10 0.20
49 3 0.06
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (47 bp):
GATTTCTGATCTGGATTCTGTTCTGATACGATACTGAATTATGTTCT
Found at i:32873 original size:24 final size:24
Alignment explanation
Indices: 32796--32891 Score: 99
Period size: 24 Copynumber: 4.0 Consensus size: 24
32786 ATTTCTGAAT
*
32796 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
* *
32818 CCTGAATTATGTTCTGAT-TCTGATC
1 --TGAATTCTGTTCTGATATCTGATA
*
32843 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
32867 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
32891 T
1 T
32892 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 14 0.23
24 44 0.73
25 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:35061 original size:18 final size:18
Alignment explanation
Indices: 35040--35093 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
35030 CGACCCATTT
35040 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
** *
35058 ACCCGACTTGTTGAACCG
1 ACCCGACCCGTTGACCCG
*
35076 ACCGTTGACCCGTTGACC
1 ACC--CGACCCGTTGACC
35094 GTTGACCGGC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 18 0.67
20 9 0.33
ACGTcount: A:0.19, C:0.41, G:0.22, T:0.19
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:35062 original size:13 final size:13
Alignment explanation
Indices: 35026--35062 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
35016 AACCAGACCC
*
35026 GACCCGACCCATT
1 GACCCGACCCGTT
*
35039 TACCCGACCCGTT
1 GACCCGACCCGTT
35052 GACCCGACCCG
1 GACCCGACCCG
35063 ACTTGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:35095 original size:15 final size:16
Alignment explanation
Indices: 35075--35110 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
35065 TTGTTGAACC
35075 GACCGTTGACC-CGTT
1 GACCGTTGACCGCGTT
35090 GACCGTTGACCGGCGTT
1 GACCGTTGACC-GCGTT
35107 GACC
1 GACC
35111 ACTGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.14, C:0.33, G:0.31, T:0.22
Consensus pattern (16 bp):
GACCGTTGACCGCGTT
Found at i:36416 original size:18 final size:18
Alignment explanation
Indices: 36390--36424 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36380 TCAAAAGGAC
*
36390 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
36408 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
36425 CCGGATGGCA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:37551 original size:12 final size:12
Alignment explanation
Indices: 37536--37604 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
37526 GACACGTTAC
37536 CTGAATTCTGTT
1 CTGAATTCTGTT
*
37548 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
37559 CTGGATTCTGTT
1 CTGAATTCTGTT
*
37571 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
*
37583 ATGAATTCTGTT
1 CTGAATTCTGTT
* *
37595 TTGATTTCTG
1 CTGAATTCTG
37605 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 12 0.26
12 33 0.70
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.49
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:37590 original size:24 final size:23
Alignment explanation
Indices: 37537--37608 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 23
37527 ACACGTTACC
*
37537 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATTCTGATA
*
37560 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
37584 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
37608 T
1 T
37609 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 15 0.35
24 27 0.63
25 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:42145 original size:179 final size:179
Alignment explanation
Indices: 41805--42169 Score: 493
Period size: 179 Copynumber: 2.0 Consensus size: 179
41795 TAATAAATGT
* * * * *
41805 ATCGATACTTTGTGTGTTCATCCTTTTTGGCATCCATTCTGAAAAAAAAGTATCGACACAAATTT
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGAAAAAAAAGTATCGACACAAATTT
* * *
41870 AACAAATGTCGCTACATGTTATAGACATATTCTCTCATAAAACCGGTATATTTATACCTGTTACA
66 AACAAATGTCGATACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACCTGTTACA
** * * *
41935 TTGTAAATTTACCTATTATATTATAATTATGGGTTTCGATATTTTTGGG
131 TTACAAAATTACATATTACATTATAATTATGGGTTTCGATATTTTTGGG
* *
41984 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTAT-AAACATAAATTATCGACAC-AATA
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGAAA-AAAAAGTATCGACACAAAT-
* * *
42047 TTAAGAAGTGTCGATACATATTATAGACATATTCTCTCATAAAACTGGTATATGTATA-CTGGTT
64 TTAACAAATGTCGATACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACCT-GTT
* * *
42111 ATATTACAAAATTACATATTACATTATTATTATGGGTTTCGATGTTTTTGGG
128 ACATTACAAAATTACATATTACATTATAATTATGGGTTTCGATATTTTTGGG
42163 ATCGACA
1 ATCGACA
42170 TTTTTAATAA
Statistics
Matches: 162, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
178 8 0.05
179 154 0.95
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (179 bp):
ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGAAAAAAAAGTATCGACACAAATTT
AACAAATGTCGATACATATTATAGACATATTCTCTCATAAAACCGGTATATGTATACCTGTTACA
TTACAAAATTACATATTACATTATAATTATGGGTTTCGATATTTTTGGG
Found at i:43726 original size:6 final size:6
Alignment explanation
Indices: 43719--43782 Score: 83
Period size: 6 Copynumber: 10.7 Consensus size: 6
43709 GTTTGGATCA
* * * * *
43719 TCATCA TCATCA TCATCT TCATCG TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
43767 TCATCT TCATCT TCAT
1 TCATCT TCATCT TCAT
43783 TGACCGCTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.42
Consensus pattern (6 bp):
TCATCT
Found at i:43732 original size:12 final size:12
Alignment explanation
Indices: 43719--43782 Score: 101
Period size: 12 Copynumber: 5.3 Consensus size: 12
43709 GTTTGGATCA
* *
43719 TCATCATCATCA
1 TCATCTTCATCG
43731 TCATCTTCATCG
1 TCATCTTCATCG
43743 TCATCTTCATCG
1 TCATCTTCATCG
43755 TCATCTTCATCG
1 TCATCTTCATCG
*
43767 TCATCTTCATCT
1 TCATCTTCATCG
43779 TCAT
1 TCAT
43783 TGACCGCTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:45623 original size:201 final size:201
Alignment explanation
Indices: 45250--45998 Score: 1282
Period size: 201 Copynumber: 3.7 Consensus size: 201
45240 TATTTAAATT
* * * * * * *
45250 AGTATCTACACCAAATTAAAAACGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAACCGAT
1 AGTATCGACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
* * *
45315 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACATATTGATGTATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* * *
45380 GGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGACATTCATTCTGA
131 GGATCGATAATTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
45445 ACCAAA
196 ACCAAA
* *
45451 AGTATCAACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
45516 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
45581 GGATCGATAATTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
131 GGATCGATAATTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
45646 ACCAAA
196 ACCAAA
*
45652 AGTATCGACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAATCGGT
1 AGTATCGACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
45717 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
45782 GGATCGATACTTTTTATAAATGTATCAACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
131 GGATCGATAATTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
45847 ACCAAA
196 ACCAAA
*
45853 AGTATCGACACAAAATCAAAAAAGTGTTGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
* * *
45918 ATATTTATACCAGTTATATTGAAAATTTACCTATAACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
45983 GTATCGATAAATTTTA
131 GGATCGATAATTTTTA
45999 CCTATTACAT
Statistics
Matches: 521, Mismatches: 27, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
201 521 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (201 bp):
AGTATCGACACAAAATCAAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGATAATTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGG
ACCAAA
Found at i:46282 original size:19 final size:19
Alignment explanation
Indices: 46254--46302 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
46244 TTACATTCAC
46254 ATAAAAAATTATAAATCTT
1 ATAAAAAATTATAAATCTT
* *
46273 TTACAAAATTATAAATCTT
1 ATAAAAAATTATAAATCTT
46292 ATAAAAAATTA
1 ATAAAAAATTA
46303 ACCTTACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAAAATTATAAATCTT
Found at i:48122 original size:33 final size:33
Alignment explanation
Indices: 48085--48148 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
48075 TCTTAAGATT
*
48085 ACCCCTTAACACCTCAACTTCTTTCACCACTTC
1 ACCCCTCAACACCTCAACTTCTTTCACCACTTC
* *
48118 ACCCCTCAACATCTCTACTTCTTTCACCACT
1 ACCCCTCAACACCTCAACTTCTTTCACCACT
48149 CCATCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.31
Consensus pattern (33 bp):
ACCCCTCAACACCTCAACTTCTTTCACCACTTC
Found at i:48233 original size:21 final size:21
Alignment explanation
Indices: 48182--48246 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
48172 CCCCTTATGC
* * *
48182 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTTTCTCTTCGACT
48203 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
48224 CTCTCGAGTTTCTATTCGACT
1 CTCTCAAGTTTCTCTTCGACT
48245 CT
1 CT
48247 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:48349 original size:15 final size:15
Alignment explanation
Indices: 48329--48361 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
48319 ACTCTATTTT
48329 CCCTCACCATCATCC
1 CCCTCACCATCATCC
*
48344 CCCTCACCGTCATCC
1 CCCTCACCATCATCC
48359 CCC
1 CCC
48362 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.64, G:0.03, T:0.18
Consensus pattern (15 bp):
CCCTCACCATCATCC
Found at i:48676 original size:22 final size:24
Alignment explanation
Indices: 48648--48698 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
48638 AACCTGCATT
*
48648 TATAATAAA-AT-TTATAATTTTA
1 TATAATAAATATACTATAATTTTA
*
48670 TATAATAAATATACTATCATTTTA
1 TATAATAAATATACTATAATTTTA
48694 TATAA
1 TATAA
48699 AAACACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TATAATAAATATACTATAATTTTA
Done.