Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001908.1 Hibiscus syriacus cultivar Beakdansim tig00003863_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: 77134
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:243 original size:38 final size:39
Alignment explanation
Indices: 169--326 Score: 230
Period size: 38 Copynumber: 4.1 Consensus size: 39
159 AAACAGCAGC
** * *
169 TTTTGAAGAATAAGTTGCAACATTAACCTCTTCCTCAAA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
*
208 TTTTGAAGAATCGGTTACAAC-TTAACCTCTCCCTCAGA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
*
246 TTTTGAAGAATCTGTTGCAAACATTAACCTCTCCCTCAGA
1 TTTTGAAGAATCGGTTGC-AACATTAACCTCTCCCTCAGA
*
286 TTTTGAAGAATCGATTGCAACATTAA-CTCTCCCTCAGA
1 TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
324 TTT
1 TTT
327 AGACACAGAT
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
38 46 0.43
39 29 0.27
40 33 0.31
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (39 bp):
TTTTGAAGAATCGGTTGCAACATTAACCTCTCCCTCAGA
Found at i:297 original size:78 final size:77
Alignment explanation
Indices: 169--326 Score: 237
Period size: 78 Copynumber: 2.0 Consensus size: 77
159 AAACAGCAGC
* *
169 TTTTGAAGAATAAGTTGCAACATTAACCTCTTCCTCAAATTTTGAAGAATCGGTTACAAC-TTAA
1 TTTTGAAGAATAAGTTGCAACATTAACCTCTCCCTCAAATTTTGAAGAATCGATTACAACATTAA
233 CCTCTCCCTCAGA
66 -CTCTCCCTCAGA
** * *
246 TTTTGAAGAATCTGTTGCAAACATTAACCTCTCCCTCAGATTTTGAAGAATCGATTGCAACATTA
1 TTTTGAAGAATAAGTTGC-AACATTAACCTCTCCCTCAAATTTTGAAGAATCGATTACAACATTA
311 ACTCTCCCTCAGA
65 ACTCTCCCTCAGA
324 TTT
1 TTT
327 AGACACAGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
77 16 0.22
78 53 0.73
79 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (77 bp):
TTTTGAAGAATAAGTTGCAACATTAACCTCTCCCTCAAATTTTGAAGAATCGATTACAACATTAA
CTCTCCCTCAGA
Found at i:3313 original size:23 final size:23
Alignment explanation
Indices: 3287--3339 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
3277 AAGACTATGC
*
3287 TGAATGAAACATCAAAACACTGT
1 TGAATGAAACAACAAAACACTGT
3310 TGAATGAAACAACAAAACACTGT
1 TGAATGAAACAACAAAACACTGT
3333 TGAATGA
1 TGAATGA
3340 TTCAGCATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (23 bp):
TGAATGAAACAACAAAACACTGT
Found at i:3589 original size:15 final size:17
Alignment explanation
Indices: 3549--3590 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
3539 TACAGAGCCT
3549 TTGAATCATTCAGGCGA
1 TTGAATCATTCAGGCGA
*
3566 TTGAATCATTCA-GCGC
1 TTGAATCATTCAGGCGA
3582 TT-AATCATT
1 TTGAATCATT
3591 TTATTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (17 bp):
TTGAATCATTCAGGCGA
Found at i:8948 original size:67 final size:68
Alignment explanation
Indices: 8803--9009 Score: 380
Period size: 68 Copynumber: 3.1 Consensus size: 68
8793 TTTCAAATAA
8803 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
1 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
8868 ATT
66 ATT
* *
8871 TTACTATATATTAAAAATAATAAAAGTTTAGCATAAT-CAAGCAAATCATGATAATAATGAAGTC
1 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
8935 ATT
66 ATT
8938 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
1 TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
*
9003 GTT
66 ATT
9006 TTAC
1 TTAC
9010 CTAAGTATTT
Statistics
Matches: 133, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
67 65 0.49
68 68 0.51
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (68 bp):
TTACTATATATTAAAAATAATAAAAGTTTAGCATAATAAAATCAAATCATGATAATAATGAAGTC
ATT
Found at i:9798 original size:28 final size:28
Alignment explanation
Indices: 9756--9812 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
9746 CTCCGTTTAC
* *
9756 ATTATATTGTTGAGCTAGTGCTTGAAAG
1 ATTATATCGTCGAGCTAGTGCTTGAAAG
9784 ATTATATCGTCGAGCTAGTGCTTGAAAG
1 ATTATATCGTCGAGCTAGTGCTTGAAAG
9812 A
1 A
9813 ACGACGATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.35
Consensus pattern (28 bp):
ATTATATCGTCGAGCTAGTGCTTGAAAG
Found at i:21047 original size:53 final size:52
Alignment explanation
Indices: 20967--21070 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 52
20957 AATCAAACTT
* * *
20967 AAATAAATTGTTGTTTGTCTCATCTAATTTATATCCATAGCCATGATAAGGAC
1 AAATAAATTGTGGTTTGTCTCACCTAATTTACA-CCATAGCCATGATAAGGAC
*
21020 AAATAAATTGTGGTTTGTCTCACCTAATTTACAGCATAGCCATGATAAGGA
1 AAATAAATTGTGGTTTGTCTCACCTAATTTACACCATAGCCATGATAAGGA
21071 TTTTGATGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 17 0.36
53 30 0.64
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (52 bp):
AAATAAATTGTGGTTTGTCTCACCTAATTTACACCATAGCCATGATAAGGAC
Found at i:21209 original size:22 final size:20
Alignment explanation
Indices: 21184--21224 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
21174 GATGTAAAAA
21184 ATAATTTTTTCTTCTGAAAAGT
1 ATAATTTTTT-TT-TGAAAAGT
21206 ATAATTTTTTTTTGAAAAG
1 ATAATTTTTTTTTGAAAAG
21225 GTCCACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
ATAATTTTTTTTTGAAAAGT
Found at i:24691 original size:19 final size:19
Alignment explanation
Indices: 24663--24719 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
24653 GCGATTTTGA
*
24663 AAAATGTGTTGCGATAGTT
1 AAAATATGTTGCGATAGTT
24682 AAAATATGTTGCGATAGTT
1 AAAATATGTTGCGATAGTT
*
24701 AAAATATGTTGCGAGAGTT
1 AAAATATGTTGCGATAGTT
24720 TGAAAAACGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (19 bp):
AAAATATGTTGCGATAGTT
Found at i:25187 original size:21 final size:21
Alignment explanation
Indices: 25161--25240 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
25151 GATTTTGGAA
25161 AATTTCGACTATCGCAACGCG
1 AATTTCGACTATCGCAACGCG
25182 AATTTCGACTATCGCAA--CG
1 AATTTCGACTATCGCAACGCG
* **
25201 AATTTGGAAAATCGCAACGCG
1 AATTTCGACTATCGCAACGCG
*
25222 AACTTCGACTATCGCAACG
1 AATTTCGACTATCGCAACG
25241 AATTTGGACT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.32
21 34 0.68
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
AATTTCGACTATCGCAACGCG
Found at i:25204 original size:19 final size:20
Alignment explanation
Indices: 25161--25251 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
25151 GATTTTGGAA
25161 AATTTCGACTATCGCAACGCG
1 AATTTCGACTATCGCAAC-CG
25182 AATTTCGACTATCGCAA-CG
1 AATTTCGACTATCGCAACCG
* **
25201 AATTTGGAAAATCGCAACGCG
1 AATTTCGACTATCGCAAC-CG
*
25222 AACTTCGACTATCGCAA-CG
1 AATTTCGACTATCGCAACCG
*
25241 AATTTGGACTA
1 AATTTCGACTA
25252 ACGTAAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
19 27 0.46
21 32 0.54
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
AATTTCGACTATCGCAACCG
Found at i:25216 original size:40 final size:40
Alignment explanation
Indices: 25171--25248 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
25161 AATTTCGACT
*
25171 ATCGCAACGCGAATTTCGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
25211 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGA
25249 CTAACGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
Found at i:25273 original size:56 final size:59
Alignment explanation
Indices: 25164--25294 Score: 178
Period size: 56 Copynumber: 2.2 Consensus size: 59
25154 TTTGGAAAAT
* *
25164 TTCGACTATCGCAACGCGAATTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAAC
1 TTCGACTATCGCAAC-CGAATTTCGACTAACGCAAC-AATTTGAAAAATCGCAACGCGAAC
* *
25225 TTCGACTATCGCAA-CGAATTTGGACTAACG-TA-AATTTGAAAAATCGCAACGCGAAC
1 TTCGACTATCGCAACCGAATTTCGACTAACGCAACAATTTGAAAAATCGCAACGCGAAC
*
25281 TTGGACTATCGCAA
1 TTCGACTATCGCAA
25295 AATCGCGTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
56 36 0.55
58 1 0.02
59 14 0.22
61 14 0.22
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (59 bp):
TTCGACTATCGCAACCGAATTTCGACTAACGCAACAATTTGAAAAATCGCAACGCGAAC
Found at i:25522 original size:12 final size:11
Alignment explanation
Indices: 25496--25520 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25486 AAACATTCAT
25496 AAATAACAAAA
1 AAATAACAAAA
25507 AAATAACAAAA
1 AAATAACAAAA
25518 AAA
1 AAA
25521 ATGTAGCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAATAACAAAA
Found at i:26322 original size:27 final size:27
Alignment explanation
Indices: 26292--26355 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
26282 TCGCAAACAT
* *
26292 TAAAAGAATATGTTCGT-GAACAATAAA
1 TAAAAGAACAAGTT-GTCGAACAATAAA
* *
26319 TAAATGAACAAGTTTTCGAACAATAAA
1 TAAAAGAACAAGTTGTCGAACAATAAA
*
26346 TAAATGAACA
1 TAAAAGAACA
26356 CAAACAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (27 bp):
TAAAAGAACAAGTTGTCGAACAATAAA
Found at i:29391 original size:23 final size:25
Alignment explanation
Indices: 29365--29410 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29355 AATATTAAAT
*
29365 AAAAATATT-AT-ATTATATTTTGG
1 AAAAATATTGATAAATATATTTTGG
*
29388 AAAATTATTGATAAATATATTTT
1 AAAAATATTGATAAATATATTTT
29411 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 2 0.11
25 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (25 bp):
AAAAATATTGATAAATATATTTTGG
Found at i:38727 original size:22 final size:22
Alignment explanation
Indices: 38702--38763 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
38692 TCGATATCCT
*
38702 ATGAACAACATTGATACTTGTG
1 ATGAACAATATTGATACTTGTG
* *
38724 ATGAACAATATCGATACATGTG
1 ATGAACAATATTGATACTTGTG
38746 ATGAACAATATTGATACT
1 ATGAACAATATTGATACT
38764 ACTAATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (22 bp):
ATGAACAATATTGATACTTGTG
Found at i:43373 original size:32 final size:32
Alignment explanation
Indices: 43323--43439 Score: 139
Period size: 32 Copynumber: 3.6 Consensus size: 32
43313 ACATTATCAC
*
43323 TTTGGATGGCATGACACATGTTATGTCATCATT
1 TTTGG-TGTCATGACACATGTTATGTCATCATT
*
43356 TTTGGTGTCATGGCACATGTCTCA--TCATCATT
1 TTTGGTGTCATGACACATGT-T-ATGTCATCATT
* * *
43388 TTAGGAGACATGACACATGTTATGTCATCATT
1 TTTGGTGTCATGACACATGTTATGTCATCATT
*
43420 TTTGGTGTCATGGCACATGT
1 TTTGGTGTCATGACACATGT
43440 CTCATCATCA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 61 0.87
33 6 0.09
34 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (32 bp):
TTTGGTGTCATGACACATGTTATGTCATCATT
Found at i:43433 original size:64 final size:64
Alignment explanation
Indices: 43332--43466 Score: 270
Period size: 64 Copynumber: 2.1 Consensus size: 64
43322 CTTTGGATGG
43332 CATGACACATGTTATGTCATCATTTTTGGTGTCATGGCACATGTCTCATCATCATTTTAGGAGA
1 CATGACACATGTTATGTCATCATTTTTGGTGTCATGGCACATGTCTCATCATCATTTTAGGAGA
43396 CATGACACATGTTATGTCATCATTTTTGGTGTCATGGCACATGTCTCATCATCATTTTAGGAGA
1 CATGACACATGTTATGTCATCATTTTTGGTGTCATGGCACATGTCTCATCATCATTTTAGGAGA
43460 CATGACA
1 CATGACA
43467 TGACACATGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
CATGACACATGTTATGTCATCATTTTTGGTGTCATGGCACATGTCTCATCATCATTTTAGGAGA
Found at i:43448 original size:32 final size:32
Alignment explanation
Indices: 43348--43453 Score: 144
Period size: 32 Copynumber: 3.3 Consensus size: 32
43338 ACATGTTATG
43348 TCATCATTTTTGGTGTCATGGCACATGTCTCA
1 TCATCATTTTTGGTGTCATGGCACATGTCTCA
* * * *
43380 TCATCATTTTAGGAGACATGACACATGT-T-A
1 TCATCATTTTTGGTGTCATGGCACATGTCTCA
43410 TGTCATCATTTTTGGTGTCATGGCACATGTCTCA
1 --TCATCATTTTTGGTGTCATGGCACATGTCTCA
43444 TCATCATTTT
1 TCATCATTTT
43454 AGGAGACATG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 1 0.02
32 58 0.94
33 1 0.02
34 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.41
Consensus pattern (32 bp):
TCATCATTTTTGGTGTCATGGCACATGTCTCA
Found at i:50934 original size:6 final size:6
Alignment explanation
Indices: 50923--50959 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
50913 GACACGTATT
50923 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
50960 GACGAGACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:51588 original size:21 final size:21
Alignment explanation
Indices: 51564--51863 Score: 271
Period size: 21 Copynumber: 14.4 Consensus size: 21
51554 ATTTTGGACT
*
51564 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
51585 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
* * *
51606 ATCACAACGAACTTGGACT--
1 ATCGCAACGAATTTGGAATAA
51625 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
51646 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
51667 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
51688 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
51709 ATTGCAACGAATTTTGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
51730 ATCGCAACGTGAACTTCGACT--
1 ATCGCAAC--GAATTTGGAATAA
*
51751 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
51772 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
51793 ATCGCAGCGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
51814 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
51835 ATCTG-AACGAATTTGGAATAA
1 ATC-GCAACGAATTTGGAATAA
51856 ATCGCAAC
1 ATCGCAAC
51864 TTGAACTTCG
Statistics
Matches: 234, Mismatches: 27, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
19 55 0.24
20 1 0.00
21 140 0.60
22 1 0.00
23 37 0.16
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:51618 original size:19 final size:19
Alignment explanation
Indices: 51594--51635 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
51584 AATCGCAACG
51594 CGAACTTCGACTATCACAA
1 CGAACTTCGACTATCACAA
* *
51613 CGAACTTGGACTATCGCAA
1 CGAACTTCGACTATCACAA
51632 CGAA
1 CGAA
51636 TTTGGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (19 bp):
CGAACTTCGACTATCACAA
Found at i:51699 original size:63 final size:62
Alignment explanation
Indices: 51560--51946 Score: 371
Period size: 63 Copynumber: 6.2 Consensus size: 62
51550 TGCGATTTTG
* * * * *
51560 GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCACAA--CGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTC
*
51621 GACTATCGCAACGAATTTGGAATAAATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACCGAACTTGGAAT--ATCGCAACGCGAACTTC
* * * *
51684 GACTATCGCAACGAATTTGGAATAAATTGCAA-CGAATTTTGAATAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACCGAACTTGGAAT--ATCGCAACGCGAACTTC
* * * *
51747 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGC-A-GCGAATTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTC
* * **
51808 GAATAAATCGCAACGAATTTGGAATAAATCTG-AA-CGAATTTGGAATAAATCGCAACTTGAACT
1 GACT--ATCGCAACGAATTTGGAATAAATC-GCAACCGAACTTGGAAT--ATCGCAACGCGAACT
51871 TC
61 TC
* * * * *
51873 GACTATCGCAACGCGAACTTGGACT--ATTGCAACGCGAACTTGGACTATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTC
51936 GACTATCGCAA
1 GACTATCGCAA
51947 TGCGAATATG
Statistics
Matches: 274, Mismatches: 34, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
59 9 0.03
61 56 0.20
62 2 0.01
63 168 0.61
64 2 0.01
65 37 0.14
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (62 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACCGAACTTGGAATATCGCAACGCGAACTTC
Found at i:51767 original size:105 final size:105
Alignment explanation
Indices: 51646--51837 Score: 339
Period size: 105 Copynumber: 1.8 Consensus size: 105
51636 TTTGGAATAA
*
51646 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
* *
51711 TGCAACGAATTTTGAATAAATCGCAACGTGAACTTCGACT
66 CGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACT
* *
51751 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAGCGAATTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
51816 CGCAACGAATTTGGAATAAATC
66 CGCAACGAATTTGGAATAAATC
51838 TGAACGAATT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 82 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (105 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
CGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACT
Found at i:51882 original size:21 final size:21
Alignment explanation
Indices: 51856--51952 Score: 149
Period size: 21 Copynumber: 4.6 Consensus size: 21
51846 TTTGGAATAA
** *
51856 ATCGCAACTTGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
51877 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
51898 ATTGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
51919 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
51940 ATCGCAATGCGAA
1 ATCGCAACGCGAA
51953 TATGTAAATC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:51912 original size:42 final size:42
Alignment explanation
Indices: 51585--51952 Score: 171
Period size: 42 Copynumber: 8.8 Consensus size: 42
51575 TTTAGAATAA
* * *
51585 ATCGCAACGCGAACTTCGACTATCACAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTCGACT
* * * * *
51625 ATCGCAA--CGAATTTGGAATAAATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT--ATCGCAACGCGAACTTCGACT
* * * *
51665 AAATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTGGAAT
1 --ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTCGACT
* * * * *
51707 AAATTGCAA--CGAATTTTGAATAAATCGCAACGTGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT--ATCGCAACGCGAACTTCGACT
* *
51751 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT--ATCGCAACGCGAACTTCGACT
* * * * *
51793 ATCGC-A-GCGAATTTGGAATAAATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT--ATCGCAACGCGAACTTCGACT
* * **
51833 AAATCTG-AA--CGAATTTGGAATAAATCGCAACTTGAACTTCGACT
1 --ATC-GCAACGCGAACTTGGACT--ATCGCAACGCGAACTTCGACT
* *
51877 ATCGCAACGCGAACTTGGACTATTGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTCGACT
*
51919 ATCGCAACGCGAACTTGGACTATCGCAATGCGAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGCGAA
51953 TATGTAAATC
Statistics
Matches: 271, Mismatches: 37, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
38 9 0.03
40 42 0.15
41 2 0.01
42 181 0.67
43 2 0.01
44 35 0.13
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTCGACT
Found at i:52281 original size:59 final size:60
Alignment explanation
Indices: 52186--52333 Score: 154
Period size: 59 Copynumber: 2.5 Consensus size: 60
52176 TCATCATATG
** * * *** ** * *
52186 TCCCCAAACTACAACCCTCATTTTAAATTGGTCCTTAAACTTTTAAATATTCAAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAACCCTTAAAAATTTAAACATTCAAATTTAA
*
52246 -CCCCAAACTATGACTCTCATTCTAAATTAACCCTTAAAAATTTAAACATTCTAATTTAA
1 TCCCCAAACTATGACTCTCATTCTAAATTAACCCTTAAAAATTTAAACATTCAAATTTAA
* * *
52305 TCCCTAAGCTATGACTCTCTTTCTAAATT
1 TCCCCAAACTATGACTCTCATTCTAAATT
52334 GATCCCCAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 47 0.65
60 25 0.35
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTCTAAATTAACCCTTAAAAATTTAAACATTCAAATTTAA
Found at i:52332 original size:60 final size:59
Alignment explanation
Indices: 52218--52333 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
52208 TTAAATTGGT
** * *
52218 CCTTAAACTTTTAAATATTCAAATTTCACCCCAAACTATGACTCTCATTCTAAATTAAC
1 CCTTAAAAATTTAAACATTCAAATTTAACCCCAAACTATGACTCTCATTCTAAATTAAC
* * * *
52277 CCTTAAAAATTTAAACATTCTAATTTAATCCCTAAGCTATGACTCTCTTTCTAAATT
1 CCTTAAAAATTTAAACATTCAAATTTAA-CCCCAAACTATGACTCTCATTCTAAATT
52334 GATCCCCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 23 0.48
60 25 0.52
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
CCTTAAAAATTTAAACATTCAAATTTAACCCCAAACTATGACTCTCATTCTAAATTAAC
Done.