Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001125.1 Hibiscus syriacus cultivar Beakdansim tig00002225_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: 111750
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3555 original size:3 final size:3
Alignment explanation
Indices: 3547--3578 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3537 TGTATCTGGT
*
3547 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3579 GTTGATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11774 original size:14 final size:14
Alignment explanation
Indices: 11757--11787 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
11747 ATCTGTTTAT
11757 TTTAATATTTTAAA
1 TTTAATATTTTAAA
11771 TTTAATATTTTAAA
1 TTTAATATTTTAAA
11785 TTT
1 TTT
11788 TAAGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATATTTTAAA
Found at i:11787 original size:7 final size:8
Alignment explanation
Indices: 11754--11790 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
11744 TTAATCTGTT
11754 TATTTTAA
1 TATTTTAA
11762 TATTTTAA
1 TATTTTAA
11770 -A-TTTAA
1 TATTTTAA
11776 TATTTTAA
1 TATTTTAA
11784 -ATTTTAA
1 TATTTTAA
11791 GATTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
6 5 0.19
7 9 0.33
8 13 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTTAA
Found at i:14039 original size:22 final size:21
Alignment explanation
Indices: 14007--14070 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
13997 TCTCATAATC
*
14007 AAATATATTAATTGATATGATTT
1 AAATA-ATTAATTAATATGA-TT
* *
14030 AAATAATTAAATAATATTATT
1 AAATAATTAATTAATATGATT
*
14051 AAA-AATTAATAAATA-GATT
1 AAATAATTAATTAATATGATT
14070 A
1 A
14071 TCATATTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.11
20 10 0.29
21 5 0.14
22 11 0.31
23 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AAATAATTAATTAATATGATT
Found at i:14461 original size:19 final size:20
Alignment explanation
Indices: 14437--14474 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14427 ACAAAATGTT
14437 ATTTAAAA-ATAAATTATTC
1 ATTTAAAATATAAATTATTC
*
14456 ATTTAAAATGTAAATTATT
1 ATTTAAAATATAAATTATT
14475 TTAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTAAAATATAAATTATTC
Found at i:14958 original size:6 final size:6
Alignment explanation
Indices: 14947--14971 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14937 GCTCCAAGCT
14947 TTTGCA TTTGCA TTTGCA TTTGCA T
1 TTTGCA TTTGCA TTTGCA TTTGCA T
14972 GTATGTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:15063 original size:3 final size:3
Alignment explanation
Indices: 15055--15089 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
15045 TTTCGTGTAC
15055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
15090 CCATTTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16668 original size:2 final size:2
Alignment explanation
Indices: 16661--16685 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16651 AGCCAAACTT
16661 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16686 TTACTTGAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31747 original size:24 final size:24
Alignment explanation
Indices: 31717--31763 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31707 GGATAGAATT
* *
31717 AAAAATATAAGGGACATTTTTAAA
1 AAAAATACAAGGGACATATTTAAA
31741 AAAAATACAAGGGACATATTTAA
1 AAAAATACAAGGGACATATTTAA
31764 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (24 bp):
AAAAATACAAGGGACATATTTAAA
Found at i:45379 original size:24 final size:26
Alignment explanation
Indices: 45333--45412 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 26
45323 ATAATTATTT
* * *
45333 ATATATATATATATATATAATAATATTA
1 ATATATATTTA-ATTTA-AATAATATAA
45361 ATA-A-ATTTAATTTAAATAA-A-AA
1 ATATATATTTAATTTAAATAATATAA
*
45383 ATATATATTTAATTTAAAT-ATATAT
1 ATATATATTTAATTTAAATAATATAA
45408 ATATA
1 ATATA
45413 CCCGGCCCGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 19 0.43
25 10 0.23
26 4 0.09
27 1 0.02
28 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATATATTTAATTTAAATAATATAA
Found at i:45394 original size:19 final size:19
Alignment explanation
Indices: 45370--45409 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45360 AATAAATTTA
45370 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
45389 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
45408 AT
1 AT
45410 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:45454 original size:12 final size:12
Alignment explanation
Indices: 45430--45475 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
45420 CGATTCCCAG
45430 CCCAATA-CCGA
1 CCCAATACCCGA
45441 CCCAATACCCGA
1 CCCAATACCCGA
* *
45453 CCCAATACCTGG
1 CCCAATACCCGA
45465 CCCAATACCCG
1 CCCAATACCCG
45476 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:45457 original size:23 final size:24
Alignment explanation
Indices: 45430--45475 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
45420 CGATTCCCAG
45430 CCCAATACC-GACCCAATACCCGA
1 CCCAATACCTGACCCAATACCCGA
*
45453 CCCAATACCTGGCCCAATACCCG
1 CCCAATACCTGACCCAATACCCG
45476 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.30, C:0.48, G:0.11, T:0.11
Consensus pattern (24 bp):
CCCAATACCTGACCCAATACCCGA
Found at i:49659 original size:20 final size:20
Alignment explanation
Indices: 49634--49723 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
49624 CCCAGTTTTA
*
49634 AAATTCGCAACACAGAAGTC
1 AAATTCGCAACACAAAAGTC
49654 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACACAAAAGTC
49674 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACACAAAAGTC
* **
49694 AATTTCGCAACACATTAGTC
1 AAATTCGCAACACAAAAGTC
49714 AAATTCGCAA
1 AAATTCGCAA
49724 AGCACGCTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACACAAAAGTC
Found at i:49923 original size:22 final size:22
Alignment explanation
Indices: 49882--49924 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
49872 AGCGACATCC
* *
49882 GTCCCTATCTCCGACGAAATCT
1 GTCCCCATCTCCGACAAAATCT
*
49904 GTCCCCATCTCCGGCAAAATC
1 GTCCCCATCTCCGACAAAATC
49925 CATCTATCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCT
Found at i:50272 original size:20 final size:22
Alignment explanation
Indices: 50249--50295 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
50239 AAACTTAAAT
50249 TCGCAACACG-AAA-ATGAAAA
1 TCGCAACACGTAAACATGAAAA
50269 TCGC-A-ACGTAAACATGAAAA
1 TCGCAACACGTAAACATGAAAA
50289 TCGCAAC
1 TCGCAAC
50296 GCGATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 15 0.65
21 1 0.04
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (22 bp):
TCGCAACACGTAAACATGAAAA
Found at i:50318 original size:19 final size:20
Alignment explanation
Indices: 50296--50389 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 20
50286 AAATCGCAAC
50296 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
50315 GCGATTTTAATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* * * ** *
50335 GCGGTTTTCATTTTTACATT
1 GCGATTTTAAGTTTCGCGTT
* * *
50355 GCGATTTTCATTTTCGCATT
1 GCGATTTTAAGTTTCGCGTT
* *
50375 GTGAATTTAAGTTTC
1 GCGATTTTAAGTTTC
50390 AGAAACTACT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
19 8 0.13
20 53 0.87
ACGTcount: A:0.16, C:0.15, G:0.19, T:0.50
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:50331 original size:20 final size:20
Alignment explanation
Indices: 50296--50371 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
50286 AAATCGCAAC
*
50296 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
50315 GCGATTTTAATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
* ** *
50335 GCGGTTTTCATTTTTACATT
1 GCGATTTTCATTTTCGCGTT
50355 GCGATTTTCATTTTCGC
1 GCGATTTTCATTTTCGC
50372 ATTGTGAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 8 0.17
20 39 0.83
ACGTcount: A:0.13, C:0.17, G:0.20, T:0.50
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:51939 original size:45 final size:45
Alignment explanation
Indices: 51890--51982 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
51880 CCACCTCCAC
51890 CTCTACCTCCACCATCACCTATTCCATCACATCATCGAGCCTCTT
1 CTCTACCTCCACCATCACCTATTCCATCACATCATCGAGCCTCTT
51935 CTCTACCTCCACCATCACCTATTCCATCACATCATCGAGCCTCTT
1 CTCTACCTCCACCATCACCTATTCCATCACATCATCGAGCCTCTT
51980 CTC
1 CTC
51983 CACTATCACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.45, G:0.04, T:0.29
Consensus pattern (45 bp):
CTCTACCTCCACCATCACCTATTCCATCACATCATCGAGCCTCTT
Found at i:51962 original size:57 final size:57
Alignment explanation
Indices: 51856--51985 Score: 149
Period size: 45 Copynumber: 2.5 Consensus size: 57
51846 ACTTCGAGAG
* * *
51856 CCATCACCTGATCGAGCCTCTTCTCCACCTCCACCTCTACCTCCACCATCACCTATT
1 CCATCACATCATCGAGCCTCTTCTCCACCTCCACCTCTACCTACACCATCACCTATT
51913 CCATCACATCATCGAGCCTCTTCT----CT--A-C-CT--C--CACCATCACCTATT
1 CCATCACATCATCGAGCCTCTTCTCCACCTCCACCTCTACCTACACCATCACCTATT
51958 CCATCACATCATCGAGCCTCTTCTCCAC
1 CCATCACATCATCGAGCCTCTTCTCCAC
51986 TATCACCTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
45 38 0.57
47 1 0.01
49 2 0.03
50 1 0.01
51 1 0.01
53 2 0.03
57 22 0.33
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.27
Consensus pattern (57 bp):
CCATCACATCATCGAGCCTCTTCTCCACCTCCACCTCTACCTACACCATCACCTATT
Found at i:52552 original size:21 final size:21
Alignment explanation
Indices: 52525--52623 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
52515 GATGCACCTA
*
52525 TCATCGTTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
52546 TTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
52567 TCATC-ATCGAAGAGGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * * *
52588 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
52609 TCATCATTCAAGAGG
1 TCATCGTTCAAGAGG
52624 TCCCGCCCGC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.03
21 60 0.94
22 2 0.03
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:52596 original size:42 final size:42
Alignment explanation
Indices: 52550--52643 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
52540 CGCCTCTTAT
* *
52550 CGTTCAAGAGGCCCCTCTCATCA-TCGAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCACTCTCATCATTC-AAGAGGCCCCGCCCAC
* * *
52592 CGTTCAAGAGGCCACTGTCATCATTCAAGAGGTCCCGCCCGC
1 CGTTCAAGAGGCCACTCTCATCATTCAAGAGGCCCCGCCCAC
52634 CGTTCAAGAG
1 CGTTCAAGAG
52644 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.18
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTCTCATCATTCAAGAGGCCCCGCCCAC
Found at i:56544 original size:25 final size:24
Alignment explanation
Indices: 56495--56541 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
56485 ATTAAGAATG
*
56495 TAAATTTTAATATTATAAATAAAT
1 TAAATTTTAAAATTATAAATAAAT
56519 TAAATTTTATAAATTAT-AATAAA
1 TAAATTTTA-AAATTATAAATAAA
56542 ATTTTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAATTTTAAAATTATAAATAAAT
Found at i:56558 original size:20 final size:20
Alignment explanation
Indices: 56507--56548 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
56497 AATTTTAATA
*
56507 TTATAAA-TA-AATTAAATT
1 TTATAAATTATAATAAAATT
56525 TTATAAATTATAATAAAATT
1 TTATAAATTATAATAAAATT
56545 TTAT
1 TTAT
56549 CATATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 2 0.10
20 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATAAATTATAATAAAATT
Found at i:57595 original size:21 final size:22
Alignment explanation
Indices: 57562--57615 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
57552 AAGGTGGAAT
*
57562 TATA-TAATATTTTAAAATTAA
1 TATATTAATATTTTAAAATAAA
* *
57583 TA-ATTAATTTTTTATAATAAA
1 TATATTAATATTTTAAAATAAA
57604 TATATTAATATT
1 TATATTAATATT
57616 AAATAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 18 0.67
22 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATTAATATTTTAAAATAAA
Found at i:64082 original size:22 final size:23
Alignment explanation
Indices: 64054--64118 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
64044 TTTTGGTGCA
*
64054 GAGGGAATCGA-TCCCCCCTCAT
1 GAGGGAACCGATTCCCCCCTCAT
* *
64076 GAGGGAACCGATTTCCCCCT-TT
1 GAGGGAACCGATTCCCCCCTCAT
64098 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
64119 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.33
23 8 0.22
24 16 0.44
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (23 bp):
GAGGGAACCGATTCCCCCCTCAT
Found at i:64139 original size:20 final size:21
Alignment explanation
Indices: 64100--64139 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
64090 CCCCCTTTGA
*
64100 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
64121 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
64140 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:65986 original size:282 final size:282
Alignment explanation
Indices: 65482--66046 Score: 1064
Period size: 282 Copynumber: 2.0 Consensus size: 282
65472 CTTCACTAGT
*
65482 TACGGTTGTATCCTTAGTAATCTCTTTTCTAAAGCCGAGCTTTGAGTTGGTCTAGATGCCTCATT
1 TACGGTTGTATCCTTAGTAATCTCTTTTCTAAAGCCGAGCTTCGAGTTGGTCTAGATGCCTCATT
65547 TCCTCTTAAGAAACAAATCAATCTTCTTCTTTAACAAGAGCGGGATGGTCAAAAATAAAGAAACC
66 TCCTCTTAAGAAACAAATCAATCTTCTTCTTTAACAAGAGCGGGATGGTCAAAAATAAAGAAACC
65612 TGTGAATGGGTTCGATCTTCTGCACTACTCCGGGAGCTAGTTCTTCACAAGCTCCACTCGAAGCT
131 TGTGAATGGGTTCGATCTTCTGCACTACTCCGGGAGCTAGTTCTTCACAAGCTCCACTCGAAGCT
65677 GACGAAGATCCAGAGTTTGAACAATTAATGAGGGATATCGATGAAGCCGAAGATGAGCCTGAGCA
196 GACGAAGATCCAGAGTTTGAACAATTAATGAGGGATATCGATGAAGCCGAAGATGAGCCTGAGCA
65742 ACCCGAGGAGCACGCACAACAG
261 ACCCGAGGAGCACGCACAACAG
*
65764 TACGGTTGTATCCTTAGTAATCTCTTTTCTAAAGCCGAGCTTCGAGTTGGTCTAGATGCCTCCTT
1 TACGGTTGTATCCTTAGTAATCTCTTTTCTAAAGCCGAGCTTCGAGTTGGTCTAGATGCCTCATT
65829 TCCTCTTAAGAAAC-AATCAATCTTCTTTCTTTAACAAGAGC-GGATGGGTC-AAAATAAAGAAA
66 TCCTCTTAAGAAACAAATCAATCTTC-TTCTTTAACAAGAGCGGGAT-GGTCAAAAATAAAGAAA
65891 CCTGTGAATGGGTTCGATCTTCTGCAACTACTCCGGGAGCTAGTTCTTCACAAGCTCCACTCGAA
129 CCTGTGAATGGGTTCGATCTTCTGC-ACTACTCCGGGAGCTAGTTCTTCACAAGCTCCACTCGAA
65956 GCTGACGAAGATCCAGAGTTTGAACAATTAATGAGGGATATCGATGAAGCCGAAGATGAGCCTGA
193 GCTGACGAAGATCCAGAGTTTGAACAATTAATGAGGGATATCGATGAAGCCGAAGATGAGCCTGA
66021 GCAACCCGAGGAGCACGCACAACAG
258 GCAACCCGAGGAGCACGCACAACAG
66046 T
1 T
66047 CGAATCAAAT
Statistics
Matches: 278, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
281 52 0.19
282 226 0.81
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (282 bp):
TACGGTTGTATCCTTAGTAATCTCTTTTCTAAAGCCGAGCTTCGAGTTGGTCTAGATGCCTCATT
TCCTCTTAAGAAACAAATCAATCTTCTTCTTTAACAAGAGCGGGATGGTCAAAAATAAAGAAACC
TGTGAATGGGTTCGATCTTCTGCACTACTCCGGGAGCTAGTTCTTCACAAGCTCCACTCGAAGCT
GACGAAGATCCAGAGTTTGAACAATTAATGAGGGATATCGATGAAGCCGAAGATGAGCCTGAGCA
ACCCGAGGAGCACGCACAACAG
Found at i:67705 original size:84 final size:84
Alignment explanation
Indices: 67564--67731 Score: 286
Period size: 84 Copynumber: 2.0 Consensus size: 84
67554 AAACAAATGA
67564 ATTTGTTGGAAAATCCTTAGTATGGATAACTAAGGTAGGACGTAGACTTTGATTGAGAAAGTCGA
1 ATTTGTTGGAAAATCCTTAGTATGGATAACTAAGGTAGGACGTAGACTTTGATTGAGAAAGTCGA
67629 ACCACTCTAAATCGCTGTG
66 ACCACTCTAAATCGCTGTG
* *
67648 ATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGAC-TAGAC-TTGATTGAGAAAGTC
1 ATTTGTTGGAAAATCCTTAGTATGGATAACTAAGGTA--GGACGTAGACTTTGATTGAGAAAGTC
67711 GAACCACTCTAAATCGCTGTG
64 GAACCACTCTAAATCGCTGTG
67732 CAATTACTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
84 71 0.89
85 5 0.06
86 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (84 bp):
ATTTGTTGGAAAATCCTTAGTATGGATAACTAAGGTAGGACGTAGACTTTGATTGAGAAAGTCGA
ACCACTCTAAATCGCTGTG
Found at i:68901 original size:32 final size:32
Alignment explanation
Indices: 68860--68920 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
68850 ATAGAGCGGC
68860 TCGGTTGTCACTGGTAAGAGCGCTGAGCCGAA
1 TCGGTTGTCACTGGTAAGAGCGCTGAGCCGAA
68892 TCGGTTGTCACTGGTAAGAGCGCTGAGCC
1 TCGGTTGTCACTGGTAAGAGCGCTGAGCC
68921 AGGGGTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (32 bp):
TCGGTTGTCACTGGTAAGAGCGCTGAGCCGAA
Found at i:69832 original size:222 final size:222
Alignment explanation
Indices: 69446--69889 Score: 852
Period size: 222 Copynumber: 2.0 Consensus size: 222
69436 TGTTTAGTGA
* *
69446 GTGAAATAGAAAATATAGTAAAATAAAGTGACGAAATTTGTATTTTACCCCAAAAAAATTTCTTT
1 GTGAAATAGAAAACATAGTAAAATAAAGTGACGAAATATGTATTTTACCCCAAAAAAATTTCTTT
69511 CCGTCAAAGTCTTCTCTCCAGTGGAGATGTACTTCCTCATTTTGGCCTTCAAAACTGAGCTGAGT
66 CCGTCAAAGTCTTCTCTCCAGTGGAGATGTACTTCCTCATTTTGGCCTTCAAAACTGAGCTGAGT
* *
69576 CTGCCTTCAAATCAGAGCCTTCAGGTTTGAAAACGCTGCGCTTATGCAAGATCTAGATTTCAGAA
131 CTGCCTTCAAATCAGAGCCTTCAGGTTCGAAAACGCTGCGCTTAAGCAAGATCTAGATTTCAGAA
69641 TGGAAGAAGAGAAAGGAGAGCTTGGGC
196 TGGAAGAAGAGAAAGGAGAGCTTGGGC
69668 GTGAAATAGAAAACATAGTAAAATAAAGTGACGAAATATGTATTTTACCCCAAAAAAATTTCTTT
1 GTGAAATAGAAAACATAGTAAAATAAAGTGACGAAATATGTATTTTACCCCAAAAAAATTTCTTT
69733 CCGTCAAAGTCTTCTCTCCAGTGGAGATGTACTTCCTCATTTTGGCCTTCAAAACTGAGCTGAGT
66 CCGTCAAAGTCTTCTCTCCAGTGGAGATGTACTTCCTCATTTTGGCCTTCAAAACTGAGCTGAGT
69798 CTGCCTTCAAATCAGAGCCTTCAGGTTCGAAAACGCTGCGCTTAAGCAAGATCTAGATTTCAGAA
131 CTGCCTTCAAATCAGAGCCTTCAGGTTCGAAAACGCTGCGCTTAAGCAAGATCTAGATTTCAGAA
69863 TGGAAGAAGAGAAAGGAGAGCTTGGGC
196 TGGAAGAAGAGAAAGGAGAGCTTGGGC
69890 AGAGCTTGAT
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 218 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (222 bp):
GTGAAATAGAAAACATAGTAAAATAAAGTGACGAAATATGTATTTTACCCCAAAAAAATTTCTTT
CCGTCAAAGTCTTCTCTCCAGTGGAGATGTACTTCCTCATTTTGGCCTTCAAAACTGAGCTGAGT
CTGCCTTCAAATCAGAGCCTTCAGGTTCGAAAACGCTGCGCTTAAGCAAGATCTAGATTTCAGAA
TGGAAGAAGAGAAAGGAGAGCTTGGGC
Found at i:91414 original size:10 final size:10
Alignment explanation
Indices: 91395--91482 Score: 59
Period size: 10 Copynumber: 8.1 Consensus size: 10
91385 TCGTTTATTG
91395 TGTTCGTTTA
1 TGTTCGTTTA
*
91405 TGTTCTTTTA
1 TGTTCGTTTA
* *
91415 GGTCCGTTTA
1 TGTTCGTTTA
*
91425 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
91438 TATTCGTTTA
1 TGTTCGTTTA
*
91448 TGTCCGTTTA
1 TGTTCGTTTA
91458 TTTGTGTTCGTTTA
1 ----TGTTCGTTTA
91472 TGTTCGTTTA
1 TGTTCGTTTA
91482 T
1 T
91483 CATTTAAATG
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
10 41 0.69
11 1 0.02
12 1 0.02
13 7 0.12
14 9 0.15
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:94192 original size:30 final size:29
Alignment explanation
Indices: 94136--94198 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
94126 GAAGAACCTA
*
94136 TCCAGAGGTCACACAGACCCCGGTAACTG
1 TCCAGAGGTCACAAAGACCCCGGTAACTG
* *
94165 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
94195 TCCA
1 TCCA
94199 TATGTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (29 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTG
Found at i:94229 original size:31 final size:30
Alignment explanation
Indices: 94187--94284 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
94177 AAAGATCCTC
*
94187 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
94217 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
94248 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
94280 GGTAA
1 GGTAA
94285 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:95653 original size:21 final size:21
Alignment explanation
Indices: 95623--95667 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
95613 ATTCTGTCGT
* *
95623 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
95644 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
95665 TTG
1 TTG
95668 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:96587 original size:36 final size:35
Alignment explanation
Indices: 96537--96676 Score: 151
Period size: 36 Copynumber: 3.9 Consensus size: 35
96527 TGAATAAGAA
* *
96537 GAACGAAAGGAAGCATCAGCACTTCCGATTCAAAAT
1 GAACGAAAGAAAGCATC-GCACTTTCGATTCAAAAT
*
96573 GAACGGAAGAAAGCATCGGCACTTTCGATTCAAGAA-
1 GAACGAAAGAAAGCATC-GCACTTTCGATTCAA-AAT
* *
96609 GAACGAAAGGAAGCATCGACACTTTCGATTC-AAGT
1 GAACGAAAGAAAGCATCG-CACTTTCGATTCAAAAT
*
96644 GAACGGAAGGAAA-CATCCGCACTTTCGATTCAA
1 GAAC-GAAAGAAAGCAT-CGCACTTTCGATTCAA
96677 TTGTTCATCT
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
34 1 0.01
35 21 0.24
36 65 0.73
37 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (35 bp):
GAACGAAAGAAAGCATCGCACTTTCGATTCAAAAT
Found at i:96623 original size:72 final size:71
Alignment explanation
Indices: 96532--96676 Score: 222
Period size: 72 Copynumber: 2.0 Consensus size: 71
96522 GAAGGTGAAT
*
96532 AAGAAGAACGAAAGGAAGCATC-AGCACTTCCGATTCAAAATGAACGGAA-GAAAGCATCGGCAC
1 AAGAAGAACGAAAGGAAGCATCGA-CACTTCCGATTC-AAATGAACGGAAGGAAA-CATCCGCAC
96595 TTTCGATTC
63 TTTCGATTC
* *
96604 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAACATCCGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTCCGATTCAAATGAACGGAAGGAAACATCCGCACTTT
96669 CGATTC
66 CGATTC
96675 AA
1 AA
96677 TTGTTCATCT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
71 30 0.44
72 37 0.54
73 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGACACTTCCGATTCAAATGAACGGAAGGAAACATCCGCACTTT
CGATTC
Found at i:98126 original size:47 final size:47
Alignment explanation
Indices: 98068--98172 Score: 201
Period size: 47 Copynumber: 2.2 Consensus size: 47
98058 TTATAGTTCT
*
98068 TAGTTCAGGTTGAATTTGCACATATAATTAGCAATGGATCGATGATC
1 TAGTTCTGGTTGAATTTGCACATATAATTAGCAATGGATCGATGATC
98115 TAGTTCTGGTTGAATTTGCACATATAATTAGCAATGGATCGATGATC
1 TAGTTCTGGTTGAATTTGCACATATAATTAGCAATGGATCGATGATC
98162 TAGTTCTGGTT
1 TAGTTCTGGTT
98173 CTGAAAGCGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (47 bp):
TAGTTCTGGTTGAATTTGCACATATAATTAGCAATGGATCGATGATC
Found at i:107131 original size:2 final size:2
Alignment explanation
Indices: 107126--107152 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
107116 ACACACACAC
107126 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 A
107153 AACTCAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:107196 original size:2 final size:2
Alignment explanation
Indices: 107189--107220 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
107179 GGCCACTTCA
107189 AT AT 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
107221 TAACAGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.