Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005430.1 Hibiscus syriacus cultivar Beakdansim tig00012451_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: 63436
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2440 original size:83 final size:83
Alignment explanation
Indices: 2282--2442 Score: 218
Period size: 83 Copynumber: 1.9 Consensus size: 83
2272 ACGACACACG
* * * * *
2282 AATGTGTGTCATCTTCATTTATGATGGGGCTTCAATGACACGCAATGTAAGTATACATGCGTGTC
1 AATGTGTGTCATCTTCATTTATGACGGGGCTTCAATGACACACAATGTAAGTATAAATGCGCGCC
2347 ATAAATTTATGACACAAA
66 ATAAATTTATGACACAAA
* *
2365 AATGTGTGTCAT-TTCATTTATGACGGGGCTTCAATGACGCACAATGCT-CGTCATAAATGCGCG
1 AATGTGTGTCATCTTCATTTATGACGGGGCTTCAATGACACACAATG-TAAGT-ATAAATGCGCG
*
2428 CCATAGATTTATGAC
64 CCATAAATTTATGAC
2443 GCACAATTGC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 33 0.49
83 35 0.51
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (83 bp):
AATGTGTGTCATCTTCATTTATGACGGGGCTTCAATGACACACAATGTAAGTATAAATGCGCGCC
ATAAATTTATGACACAAA
Found at i:8062 original size:17 final size:17
Alignment explanation
Indices: 8030--8063 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8020 TAATGTGAAC
* *
8030 TTATTATTATTTAAAAT
1 TTATTATTAATAAAAAT
8047 TTATTATTAATAAAAAT
1 TTATTATTAATAAAAAT
8064 ATAAAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTATTAATAAAAAT
Found at i:11020 original size:23 final size:23
Alignment explanation
Indices: 10994--11039 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
10984 TCTCCGCCGG
10994 GTGGAAGATGAAACCACCACCGC
1 GTGGAAGATGAAACCACCACCGC
11017 GTGGAAGATGAAACCACCACCGC
1 GTGGAAGATGAAACCACCACCGC
11040 AAACCAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.26, T:0.09
Consensus pattern (23 bp):
GTGGAAGATGAAACCACCACCGC
Found at i:16381 original size:21 final size:21
Alignment explanation
Indices: 16355--16394 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16345 CAGAACCCCA
*
16355 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
16376 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
16395 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:16446 original size:21 final size:22
Alignment explanation
Indices: 16378--16436 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
16368 TCCCCTGTGG
16378 GGGGAATCGGTTCCCCTTCAAA
1 GGGGAATCGGTTCCCCTTCAAA
16400 GGGGAATCGGTTCCCCTTCAAA
1 GGGGAATCGGTTCCCCTTCAAA
16422 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
16437 TCAGGGGGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAA
Found at i:26750 original size:2 final size:2
Alignment explanation
Indices: 26743--26769 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26733 GGAATTTAAG
26743 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
26770 ATGCTTTATT
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:30798 original size:31 final size:31
Alignment explanation
Indices: 30763--30838 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
30753 AATAGGTGAA
** *
30763 TCTGTCAGGAATTTGTGACAGATCCATATAT
1 TCTGTCACAAATTTGTGACAGATCCACATAT
* *
30794 TCTGTCACAAATTTGTGATAGGTCCACATAT
1 TCTGTCACAAATTTGTGACAGATCCACATAT
**
30825 TCCATCACAAATTT
1 TCTGTCACAAATTT
30839 AAAAACTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (31 bp):
TCTGTCACAAATTTGTGACAGATCCACATAT
Found at i:42664 original size:41 final size:41
Alignment explanation
Indices: 42596--42680 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
42586 ATATTCTAGT
*
42596 GTGGCTTTGTTGGTGTAGTCCCGCAGAGAAGATTT-AGAAGA
1 GTGGCTTTGTTGGTGTAGTCCCACAGAGAAGATTTGA-AAGA
* *
42637 GTGGCTTTGTTGGTGTGGTCTCACAGAGAAGATTTGAAAGA
1 GTGGCTTTGTTGGTGTAGTCCCACAGAGAAGATTTGAAAGA
42678 GTG
1 GTG
42681 AATTTCTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 39 0.98
42 1 0.03
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.31
Consensus pattern (41 bp):
GTGGCTTTGTTGGTGTAGTCCCACAGAGAAGATTTGAAAGA
Found at i:44534 original size:15 final size:15
Alignment explanation
Indices: 44511--44547 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
44501 AACAACACTG
44511 ATAAATATAAT-TAA
1 ATAAATATAATGTAA
44525 ATATAATATAATGTAA
1 ATA-AATATAATGTAA
44541 ATAAATA
1 ATAAATA
44548 AATATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
ATAAATATAATGTAA
Found at i:50208 original size:3 final size:3
Alignment explanation
Indices: 50200--50291 Score: 157
Period size: 3 Copynumber: 30.7 Consensus size: 3
50190 TTAATATATT
* *
50200 TAA TAA TAA TAG 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
*
50248 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
50292 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51193 original size:113 final size:113
Alignment explanation
Indices: 50431--51758 Score: 1653
Period size: 113 Copynumber: 11.7 Consensus size: 113
50421 ATTGAATAAA
* * **
50431 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGA-TG-ATCCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TACTGGAAAT-ACTGAAT-CA
* *
50493 TCAAATGATGAATTCAAGCAAAAGTTTGAACAAGTTCTTCTCATTATGAAC
63 TCGAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
50544 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-TCT-CTGGAAA-AGAT-AATC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTTACTGGAAATA-CTGAAT-
* * *
50605 CATC-AATTTAATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
61 CATCGAA--TGATGAATTCAAG-CAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
50659 TTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACTTTCT-CTGGAAA-AGCTG-ATCCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TACTGGAAATA-CTGAAT-CA
* * *
50721 TC-AATTTGATGACTTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
63 TCGAA--TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
50773 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAA-AGAT-AATCCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TACTGGAAATA-CTGAAT-CA
* *
50835 TC-AATTTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
63 TCGAA--TGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
50887 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCT-CTGGAAA-AGCTG-AT
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTT-TACTGGAAATA-CTGAAT
* * * *
50949 CCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
61 -CATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
51003 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCT-CTGGAAATGCTGAATC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTT-TACTGGAAATACTGAATC
* * *
51067 ATCGAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
51119 TTCTTATTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
*
51184 AATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
** *** * *
51232 TTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
* * *
51297 AATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCA-TATGAAC
66 AATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
51344 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTTTTACTGGAAATACTGAATCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
51409 AATGATGAA-TCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAAC
** *** * *
51456 TTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
* * *
51521 AATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
51569 TTCTTCTTCCATCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
51634 AATGATGAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGAATTCAAGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAAC
** *** * *
51682 TTCTTCTTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATC
1 TTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATC
51747 GAATGATGAATT
65 GAATGATGAATT
51759 TATATCTTTG
Statistics
Matches: 1096, Mismatches: 90, Indels: 57
0.88 0.07 0.05
Matches are distributed among these distances:
111 22 0.02
112 175 0.16
113 320 0.29
114 284 0.26
115 61 0.06
116 168 0.15
117 64 0.06
118 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCG
AATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:51551 original size:450 final size:450
Alignment explanation
Indices: 50431--51760 Score: 1888
Period size: 450 Copynumber: 2.9 Consensus size: 450
50421 ATTGAATAAA
* **
50431 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGA-TGATCCAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAT-ACTGATCCAT
50494 CAAATGATGAATTCAAGC-AAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
64 CAAATGATGAA-TCAAGCGAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
* * *
50558 TCAGATGACGAGTTCTTCTCATTATGAACTCTCTGGAAAAGAT-AATCCATC-AATTTAATGAAT
127 TCAGAT-A-GAGTTCTTCTCATTATGAACTCTCTGGAAATGCTGAAT-CATCGAA--TGATGAAT
* *
50621 TCAGAA-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTC
187 TTA-AACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
* * * *
50685 TTCTCATTATGAACTTTCT-CTGGAAA-AGCTG-ATCCATC-AATTTGATGACTTCAGGTAAAAG
251 TTCTCATTATGAACTTT-TACTGGAAATA-CTGAAT-CATCGAA--TGATGAATTCAAGCAAAAA
**
50746 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
311 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGA
**** * * * * *** *
50811 ACTTTCTCTGGAAAAGAT-AATCCATC-AATTTGATGAATTCAGGTAAAAGGTTGAACAAGTTCT
376 ACTCGAACTGGTAATGCTGAAT-CATCGAA--TGATGAATTTAAACAAAAGGTTGAACAAATTCT
50874 TCTCATTATGAAC
438 TCTCATTATGAAC
50887 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AGCTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCTCTGGAAATA-CTGATCC
*
50951 ATCAAATGATGGATTC-AG-GTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
62 ATCAAATGAT-GAATCAAGCG-AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
51014 TCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGAATCATCGAATGATGA
124 TCTTCAGAT-A-GAGTTCTTCTCATTATGAAC--TCTCTGGAAATGCTGAATCATCGAATGATGA
* *
51079 ATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTTAGATGAGTT
185 ATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
51144 CTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCGAATGATGAATTCAAGCAAAAAGTTG
250 CTTCTCATTATGAACTTTTACTGGAAATACTGAATCATCGAATGATGAATTCAAGCAAAAAGTTG
51209 AACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTC
315 AACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTC
51274 GAACTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCA-T
380 GAACTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATT
51338 ATGAAC
445 ATGAAC
*
51344 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-TTTTTACTGGAAATACTGAAT-CAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAATACTG-ATCCAT
* **
51407 CGAATGATGAATCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTC
64 CAAATGATGAATCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
51472 AGAT-GAGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAA
129 AGATAGAGTTCTTCTCATTATGAACTC--TCTGGAAATGCTGAATCATCGAATGATGAATTTAAA
*
51536 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTCTCA
192 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
51601 TTATGAACTTTTACTGGAAATACTGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGT
257 TTATGAACTTTTACTGGAAATACTGAATCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGT
51666 TCTTCTCATTATGAACTTCTTCTTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
322 TCTTCTCATTATGAACTTCTTC-TTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
51731 GTAATGCTGAATCATCGAATGATGAATTTA
386 GTAATGCTGAATCATCGAATGATGAATTTA
51761 TATCTTTGCT
Statistics
Matches: 805, Mismatches: 40, Indels: 63
0.89 0.04 0.07
Matches are distributed among these distances:
448 2 0.00
450 202 0.25
451 72 0.09
453 53 0.07
454 45 0.06
455 4 0.00
456 6 0.01
457 40 0.05
458 35 0.04
459 192 0.24
460 128 0.16
461 21 0.03
462 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (450 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATACTGATCCATCA
AATGATGAATCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATAGAGTTCTTCTCATTATGAACTCTCTGGAAATGCTGAATCATCGAATGATGAATTTAAACAAA
AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTTACTGGAAATACTGAATCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTT
CTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGTAAT
GCTGAATCATCGAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:52184 original size:22 final size:22
Alignment explanation
Indices: 52159--52213 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
52149 CATAAAGTTT
*
52159 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
52181 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
52203 TCATCTTTGAA
1 TCATCTTTGAA
52214 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:52656 original size:40 final size:40
Alignment explanation
Indices: 52600--52679 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
52590 TTTCAGCTTA
52600 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
* **
52640 GATGTAAAACATTTGACAATGCATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
52680 ACTCTGCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
Found at i:55001 original size:114 final size:114
Alignment explanation
Indices: 54801--55126 Score: 494
Period size: 114 Copynumber: 2.9 Consensus size: 114
54791 GATCATGCAG
* * * * * * * *
54801 TTCATCTTTCAATTTCAATGATTGGTTATGG-GATTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGATTTTGGAG-TTCATACCAAATCAGATTAGATAATTCAAAG
* * * *
54865 AATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
*
54915 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATTAGATAATTCAAAGA
1 TTCATCTTTCAAATTCAATGATTGATTTTGGAGTTCATACCAAATCAGATTAGATAATTCAAAGA
54980 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
*
55029 TTCATCTTCCAAATTCAATGATTGA-TTTGGAGTTCATACCAAATCAGATTAGATAATTCAAAGA
1 TTCATCTTTCAAATTCAATGATTGATTTTGGAGTTCATACCAAATCAGATTAGATAATTCAAAGA
*
55093 ACACTTCCAGAAGATGCTATTGAGCCTCATTATT
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATT
55127 CTTCCAAATT
Statistics
Matches: 195, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
113 72 0.37
114 122 0.63
115 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATTCAATGATTGATTTTGGAGTTCATACCAAATCAGATTAGATAATTCAAAGA
ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:55196 original size:95 final size:93
Alignment explanation
Indices: 55033--55221 Score: 281
Period size: 95 Copynumber: 2.0 Consensus size: 93
55023 AGCAAATTCA
* * *
55033 TCTTCCAAATTCAATGATTGATTTGGAGTTCATACCAAATCAGATTAGATAATTCAAAGAACACT
1 TCTTCCAAATTCAATGATTGATTTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGAACACT
55098 TCCAGAAGATGCTATTGAGCCTCATTAT
66 TCCAGAAGATGCTATTGAGCCTCATTAT
*
55126 TCTTCCAAATTCAATGATTGGTTTTGTG-GTTTCATACCAAACCAGATCAGATAACTCAAAGAAC
1 TCTTCCAAATTCAATGATT-GATTTG-GAG-TTCATACCAAACCAGATCAGATAACTCAAAGAAC
* * *
55190 ATTTCCAGAAGATGCTATTGAGTCTCCTTAT
63 ACTTCCAGAAGATGCTATTGAGCCTCATTAT
55221 T
1 T
55222 TCTACTACGA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
93 19 0.22
94 6 0.07
95 61 0.71
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (93 bp):
TCTTCCAAATTCAATGATTGATTTGGAGTTCATACCAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGAGCCTCATTAT
Done.