Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006442.1 Hibiscus syriacus cultivar Beakdansim tig00015562_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: 47134
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2866 original size:35 final size:35
Alignment explanation
Indices: 2792--2872 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 35
2782 ATGGTGATGA
* *
2792 AATGGTAATGGAAAGGATGATGTTATTGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
2827 -ATGGTGATGGAATATGG-TGATGATA-TGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATTGGCGTGAT
2861 AATGGTGATGGA
1 AATGGTGATGGA
2873 CAGATTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 20 0.49
35 19 0.46
36 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
Found at i:7774 original size:18 final size:18
Alignment explanation
Indices: 7751--7793 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
7741 CGGTTTAGAA
7751 ATGGTTAAGGTATAGGAT
1 ATGGTTAAGGTATAGGAT
7769 ATGGTTAAGGTATAGGAT
1 ATGGTTAAGGTATAGGAT
7787 ATGGTTA
1 ATGGTTA
7794 TGATAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (18 bp):
ATGGTTAAGGTATAGGAT
Found at i:8488 original size:11 final size:11
Alignment explanation
Indices: 8474--8562 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 11
8464 GGATGATTTA
8474 ATGGTGATGAT
1 ATGGTGATGAT
*
8485 ATGGTAATGGA-
1 ATGGTGAT-GAT
*
8496 A-GGATGATGTT
1 ATGG-TGATGAT
*
8507 ATTGGCG-TGAT
1 A-TGGTGATGAT
8518 ATGGTGATGGAAT
1 ATGGTGAT-G-AT
8531 ATGGTGATGAT
1 ATGGTGATGAT
*
8542 ATAGGCG-TGAT
1 AT-GGTGATGAT
8553 AATGGTGATG
1 -ATGGTGATG
8563 GACAGATTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 21
0.67 0.09 0.24
Matches are distributed among these distances:
10 7 0.12
11 28 0.47
12 12 0.20
13 12 0.20
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (11 bp):
ATGGTGATGAT
Found at i:8503 original size:33 final size:33
Alignment explanation
Indices: 8461--8529 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
8451 GTTGATGAAT
*
8461 GAAGGATGAT-TTAATGGTGATGATATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGATATGGTAATG
* *
8494 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGATATGGTAATG
8527 GAA
1 GAA
8530 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.30, C:0.01, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGATATGGTAATG
Found at i:10100 original size:24 final size:21
Alignment explanation
Indices: 10066--10108 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
10056 TCAACAAGAT
*
10066 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
10088 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
10109 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:12256 original size:33 final size:33
Alignment explanation
Indices: 12195--12262 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
12185 GTTGATGAAT
*
12195 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
12228 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
12261 GA
1 GA
12263 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:16518 original size:33 final size:33
Alignment explanation
Indices: 16457--16524 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
16447 GTTGATGAAT
*
16457 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
16490 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
16523 GA
1 GA
16525 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:25628 original size:34 final size:34
Alignment explanation
Indices: 25589--25691 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
25579 TTGATGAATG
*
25589 AAGGATGAT-TTAATGGTGATGAAATGGTAATGGA
1 AAGGATGATGTTAATGGCG-TGAAATGGTAATGGA
* * *
25623 AAGGATGATGTTATTGGCGTGATATGGTGATGGA
1 AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
* *
25657 ATATGG-TGATGAT-ATGGCGTGATAATGGTGATGGA
1 A-A-GGATGATGTTAATGGCGTGA-AATGGTAATGGA
25692 CAGATTTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.53
35 25 0.43
36 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (34 bp):
AAGGATGATGTTAATGGCGTGAAATGGTAATGGA
Found at i:25685 original size:35 final size:35
Alignment explanation
Indices: 25611--25691 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 35
25601 ATGGTGATGA
* *
25611 AATGGTAATGGAAAGGATGATGTTATTGGCGTGAT
1 AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
25646 -ATGGTGATGGAATATGG-TGATGATA-TGGCGTGAT
1 AATGGTGATGGAA-A-GGATGATGATATTGGCGTGAT
25680 AATGGTGATGGA
1 AATGGTGATGGA
25692 CAGATTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 20 0.49
35 19 0.46
36 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGAAAGGATGATGATATTGGCGTGAT
Found at i:28597 original size:36 final size:36
Alignment explanation
Indices: 28550--28650 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
28540 GATACAATCT
28550 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
28586 GTCCATCACCATTATCACGCCTATATCA-CACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
28621 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
28651 TCCTTCCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 14 0.23
35 19 0.31
36 28 0.46
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:28665 original size:33 final size:34
Alignment explanation
Indices: 28551--28689 Score: 117
Period size: 33 Copynumber: 4.1 Consensus size: 34
28541 ATACAATCTG
* *
28551 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCATTATCACGCCAATAACATCATCC-T
* * *
28585 AGTCCATCACCATTATCACGCCTATATCACACCAT-AT
1 --TCCATCACCATTATCACGCC-A-ATAACATCATCCT
28622 TCCATCACCA-TATCACGCCAATAACATCATCCT
1 TCCATCACCATTATCACGCCAATAACATCATCCT
* * *
28655 TCCATTACCATT-TCATCACCATTAA-ATCATCCT
1 TCCATCACCATTATCA-CGCCAATAACATCATCCT
28688 TC
1 TC
28690 ATTCATCAAC
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
32 8 0.09
33 24 0.28
34 17 0.20
35 10 0.12
36 20 0.23
37 1 0.01
38 6 0.07
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCATCCT
Found at i:29107 original size:25 final size:25
Alignment explanation
Indices: 29086--29140 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
29076 ATTATCACGC
29086 CTATCATCACCATAGTCCATCACCA
1 CTATCATCACCATAGTCCATCACCA
* *
29111 TTATCATCACCATATTCCATCACCA
1 CTATCATCACCATAGTCCATCACCA
29136 -TATCA
1 CTATCA
29141 CGCCTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.29
Consensus pattern (25 bp):
CTATCATCACCATAGTCCATCACCA
Found at i:29108 original size:13 final size:12
Alignment explanation
Indices: 29090--29139 Score: 66
Period size: 13 Copynumber: 4.0 Consensus size: 12
29080 TCACGCCTAT
29090 CATCACCATAGTC
1 CATCACCATA-TC
29103 CATCACCATTAT-
1 CATCACCA-TATC
29115 CATCACCATATTC
1 CATCACCATA-TC
29128 CATCACCATATC
1 CATCACCATATC
29140 ACGCCTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.06
12 11 0.32
13 19 0.56
14 2 0.06
ACGTcount: A:0.32, C:0.38, G:0.02, T:0.28
Consensus pattern (12 bp):
CATCACCATATC
Found at i:29478 original size:495 final size:502
Alignment explanation
Indices: 28459--29479 Score: 1368
Period size: 495 Copynumber: 2.0 Consensus size: 502
28449 GGGTCAAAGT
* * *
28459 CCTTTCAT-ACCATCCCTTATATAACTTATAAGAAACGGGTCTTTGCTCCTTTATAGCATTGGTT
1 CCTTACATCACCATCCCTTATAAAACTTATAAGAAACGGGTCTTTACTCCTTTATAGCATTGGTT
28523 CCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACGCCTATATCATCACCATAGT
66 CCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACGCC-ATATCATCACCATAGT
* *
28588 CCATCACCATTATCACGCCTATATCACACCATATTCCATCACCATATCACGCCAATAACATCATC
130 CCATCACCATTAT----CC--TAT-ACACCATATTCCATCACCATATCACGCCAATAACACCAAC
** * *
28653 CTTCCATTACCATTTCATCACCATTAAATCATCCTTCATTCATCAACAAGGCATACTTCATCACC
188 CTTAAATTACCATTTCATCACCATTAAATCATCCTTCATTCACCAACAAGGCATACTCCATCACC
*
28718 ACCATTGGAGGCCGAAGTCACATCACTTGAAGGAGATTTATTCAACACTTCCGCAGCCCATCTTT
253 ACCATTGGAGGCCGAAGTCACATCACTTGAAGGAGATTTATACAACACTTCCGCAGCCCATCTTT
*
28783 GATAACTATTCTATCCATTTCAAATCTTTCCATTTCTATTTACTTTTCATTTCTTAATTATCATA
318 GATAACTATTCTATCCATTTCAAA--TTTCCATTTCCATTTAC---TCATTTCTTAATTATCATA
* * *
28848 TTACTTAATCAATTCTTTTTCTTTTTGTGCAGATTACTTTCAATCCAAGGTGTAGCATTGGTGTC
378 TTACTTAACCAATTCTTCTTC-TTTTATGCAGATTACTTTCAATCCAAGGTGTAGCATTGGTGTC
28913 TCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTGGTTAG
442 TCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTGGTTAG
*
28974 CCATACATCACCATCCCTTATAAAAACTTATAAGAAACGGGTCTTTACTCCTTTATAGCATTGGT
1 CCTTACATCACCATCCCTTAT-AAAACTTATAAGAAACGGGTCTTTACTCCTTTATAGCATTGGT
29039 TCC-TCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACGCC-TATCATCACCATAGT
65 TCCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACGCCATATCATCACCATAGT
* *
29102 CCATCACCATTAT-C-AT-CACCATATTCCATCACCATATCACGCCTATATTATCACCAACTTAT
130 CCATCACCATTATCCTATACACCATATTCCATCACCATATCACGCC-A-A-TAACACCAACCT-T
* * * * *
29164 AAATTTCCATTTCTTCATCTTTGAAAT-ATCCTTCA-TC-CCAACAAGGCATTCGTCCATCACCA
191 AAATTACCATTTCATCACCATT-AAATCATCCTTCATTCACCAACAAGGCATAC-TCCATCACCA
* ***
29226 CCATTGGAGGCCGAA-TCCATCATCACTTGAA-GA-ATCATTCTACAACACTTCCGCAGCTTTTC
254 CCATTGGAGGCCGAAGT-CA-CATCACTTGAAGGAGAT--TTATACAACACTTCCGCAGCCCATC
29288 TTTGATAACTATTCTATCCATTTC-AA-TT-C-TTTCCATTT-C-C-TTTCTT-ATTACTCAT-T
315 TTTGATAACTATTCTATCCATTTCAAATTTCCATTTCCATTTACTCATTTCTTAATTA-TCATAT
*
29344 TACTTAACCAA-TCATTCTTC-TTTATGCAGATTACTTTTCAATTCAAGGTGTAGCATTTGGTGT
379 TACTTAACCAATTC-TTCTTCTTTTATGCAGATTAC-TTTCAATCCAAGGTGTAGCA-TTGGTGT
*
29407 CTTTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTGGTTAG
441 CTCTCCTAGATCGGGAAACAACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTGGTTAG
29469 CCTTACATCAC
1 CCTTACATCAC
29480 TTATGGTGAA
Statistics
Matches: 461, Mismatches: 29, Indels: 52
0.85 0.05 0.10
Matches are distributed among these distances:
493 13 0.03
494 21 0.05
495 98 0.21
496 10 0.02
497 1 0.00
501 1 0.00
502 8 0.02
503 1 0.00
504 29 0.06
505 1 0.00
506 18 0.04
507 40 0.09
508 80 0.17
509 5 0.01
514 28 0.06
515 6 0.01
516 57 0.12
517 44 0.10
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (502 bp):
CCTTACATCACCATCCCTTATAAAACTTATAAGAAACGGGTCTTTACTCCTTTATAGCATTGGTT
CCTTCTTAGTTTTATAAGATACAATCTGTCCATCACCATTATCACGCCATATCATCACCATAGTC
CATCACCATTATCCTATACACCATATTCCATCACCATATCACGCCAATAACACCAACCTTAAATT
ACCATTTCATCACCATTAAATCATCCTTCATTCACCAACAAGGCATACTCCATCACCACCATTGG
AGGCCGAAGTCACATCACTTGAAGGAGATTTATACAACACTTCCGCAGCCCATCTTTGATAACTA
TTCTATCCATTTCAAATTTCCATTTCCATTTACTCATTTCTTAATTATCATATTACTTAACCAAT
TCTTCTTCTTTTATGCAGATTACTTTCAATCCAAGGTGTAGCATTGGTGTCTCTCCTAGATCGGG
AAACAACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTGGTTAG
Found at i:31053 original size:21 final size:22
Alignment explanation
Indices: 31011--31053 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
31001 GCAAGAAGAC
*
31011 CCATGTGCATTCATGTAGGCAT
1 CCATGTGCATTCATGTAAGCAT
*
31033 CCATGTGCA-TCATTTAAGCAT
1 CCATGTGCATTCATGTAAGCAT
31054 GTGCACTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (22 bp):
CCATGTGCATTCATGTAAGCAT
Found at i:33016 original size:33 final size:33
Alignment explanation
Indices: 32974--33042 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
32964 GTTGATGAAT
*
32974 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
33007 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
33040 GAA
1 GAA
33043 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:33047 original size:13 final size:12
Alignment explanation
Indices: 33028--33113 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
33018 TTATTGGCGT
33028 GATATGGTGATG
1 GATATGGTGATG
33040 GAATATGGTGAT-
1 G-ATATGGTGATG
*
33052 GATATAGGCG-T-
1 GATAT-GGTGATG
33063 GATAATGGTGATG
1 GAT-ATGGTGATG
33076 GACTATGGTGAT-
1 GA-TATGGTGATG
*
33088 GATATAGGCG-T-
1 GATAT-GGTGATG
33099 GATAATGGTGATG
1 GAT-ATGGTGATG
33112 GA
1 GA
33114 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:33083 original size:36 final size:36
Alignment explanation
Indices: 33013--33114 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
33003 AATGGAAGGA
* * *
33013 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
33048 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
33084 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
33115 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:38372 original size:11 final size:11
Alignment explanation
Indices: 38358--38446 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 11
38348 GGATGATTTA
38358 ATGGTGATGAT
1 ATGGTGATGAT
*
38369 ATGGTAATGGA-
1 ATGGTGAT-GAT
*
38380 A-GGATGATGTT
1 ATGG-TGATGAT
*
38391 ATTGGCG-TGAT
1 A-TGGTGATGAT
38402 ATGGTGATGGAAT
1 ATGGTGAT-G-AT
38415 ATGGTGATGAT
1 ATGGTGATGAT
*
38426 ATAGGCG-TGAT
1 AT-GGTGATGAT
38437 AATGGTGATG
1 -ATGGTGATG
38447 GACAGATTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 21
0.67 0.09 0.24
Matches are distributed among these distances:
10 7 0.12
11 28 0.47
12 12 0.20
13 12 0.20
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (11 bp):
ATGGTGATGAT
Found at i:38387 original size:33 final size:33
Alignment explanation
Indices: 38345--38413 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
38335 GTTGATGAAT
*
38345 GAAGGATGAT-TTAATGGTGATGATATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGATATGGTAATG
* *
38378 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGATATGGTAATG
38411 GAA
1 GAA
38414 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.30, C:0.01, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGATATGGTAATG
Found at i:39977 original size:24 final size:21
Alignment explanation
Indices: 39943--39985 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
39933 TCAACAAGAT
*
39943 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
39965 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
39986 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:42136 original size:33 final size:33
Alignment explanation
Indices: 42075--42142 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
42065 GTTGATGAAT
*
42075 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
42108 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
42141 GA
1 GA
42143 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:46397 original size:33 final size:33
Alignment explanation
Indices: 46336--46403 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
46326 GTTGATGAAT
*
46336 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* * *
46369 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGAAATGGTAATG
46402 GA
1 GA
46404 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.01, G:0.37, T:0.31
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Done.