Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001154.1 Hibiscus syriacus cultivar Beakdansim tig00002300_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: 107966
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:8533 original size:17 final size:19
Alignment explanation
Indices: 8505--8557 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
8495 TTAATAATTT
8505 TAAAC-TATATATTTATATA
1 TAAACATATAT-TTTATATA
8524 TAAA-ATATATTTTATATA
1 TAAACATATATTTTATATA
8542 TAAACATATAATTTTA
1 TAAACATAT-ATTTTA
8558 AAATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.39
19 13 0.42
20 6 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAACATATATTTTATATA
Found at i:8570 original size:14 final size:15
Alignment explanation
Indices: 8553--8581 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8543 AAACATATAA
8553 TTTT-AAAATTATTT
1 TTTTAAAAATTATTT
8567 TTTTAAAAATTATTT
1 TTTTAAAAATTATTT
8582 CAATGATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAAATTATTT
Found at i:11981 original size:26 final size:25
Alignment explanation
Indices: 11943--11991 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
11933 CATTTCATAT
* *
11943 AAAAATATGTTTAATATATAAATAA
1 AAAAATATATTTAACATATAAATAA
11968 AAAAATTATATTTAACATATAAAT
1 AAAAA-TATATTTAACATATAAAT
11992 CAATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAAATATATTTAACATATAAATAA
Found at i:13635 original size:24 final size:24
Alignment explanation
Indices: 13590--13635 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13580 TTTTTATTGA
*
13590 ATATTTGTAATTAAATTCAACTTT
1 ATATTTGTAATTAAATTAAACTTT
13614 ATATTTGTAATTAAGA-TAAACT
1 ATATTTGTAATTAA-ATTAAACT
13636 GGTAATCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (24 bp):
ATATTTGTAATTAAATTAAACTTT
Found at i:17135 original size:6 final size:6
Alignment explanation
Indices: 17119--17152 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
17109 AGGAAGAGAA
*
17119 AAATGG GAATGG AAATGG AAATGG AAATGTG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATG-G AAA
17153 GGGTGATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:20447 original size:23 final size:23
Alignment explanation
Indices: 20414--20461 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
20404 TTTTAAGATC
*
20414 ATATTATTTATTTATTCGAAATA
1 ATATTAATTATTTATTCGAAATA
*
20437 ATATTAATTATTTATTTGAAATA
1 ATATTAATTATTTATTCGAAATA
20460 AT
1 AT
20462 GTTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
ATATTAATTATTTATTCGAAATA
Found at i:20686 original size:24 final size:24
Alignment explanation
Indices: 20631--20707 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
20621 TAAAACTTAA
20631 ATATTTTTTTATAATATTATAAAT
1 ATATTTTTTTATAATATTATAAAT
* * *
20655 ATACTTTTTTATAATGATTTTATAT
1 ATATTTTTTTATAAT-ATTATAAAT
* *
20680 A-ATTTTTATA-AAAATATATAAAT
1 ATATTTTTTTATAATAT-TATAAAT
20703 -TATTT
1 ATATTT
20708 AATTATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
22 2 0.05
23 11 0.26
24 21 0.50
25 8 0.19
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (24 bp):
ATATTTTTTTATAATATTATAAAT
Found at i:21375 original size:16 final size:16
Alignment explanation
Indices: 21354--21384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21344 TTGAAATGCA
*
21354 AAAATAACTATAAAAT
1 AAAATAACAATAAAAT
21370 AAAATAACAATAAAA
1 AAAATAACAATAAAA
21385 CATTCTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAACAATAAAAT
Found at i:23193 original size:37 final size:36
Alignment explanation
Indices: 23143--23216 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
23133 CATTAAACCT
**
23143 TTTTATATTTTTAATTTTGCAAAAAAAATTATATAAA
1 TTTTATAAATTTAATTTTGCAAAAAAAA-TATATAAA
** *
23180 TTTTATAAATTTAATTTTTTAAAGAAAATATATAAA
1 TTTTATAAATTTAATTTTGCAAAAAAAATATATAAA
23216 T
1 T
23217 ATTTTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 9 0.28
37 23 0.72
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTTATAAATTTAATTTTGCAAAAAAAATATATAAA
Found at i:25436 original size:10 final size:10
Alignment explanation
Indices: 25421--25445 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25411 CGAGATTGGA
25421 TTTTTATTAT
1 TTTTTATTAT
25431 TTTTTATTAT
1 TTTTTATTAT
25441 TTTTT
1 TTTTT
25446 TATGAATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:25739 original size:3 final size:3
Alignment explanation
Indices: 25727--25766 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
25717 TAAAAAAAGA
*
25727 AAT AAA AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25767 CAACAACAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:25750 original size:14 final size:14
Alignment explanation
Indices: 25731--25766 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
25721 AAAAGAAATA
25731 AAAATAATAATAAT
1 AAAATAATAATAAT
25745 AAAATAATAATAAT
1 AAAATAATAATAAT
25759 AATAATAA
1 AA-AATAA
25767 CAACAACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:25751 original size:20 final size:20
Alignment explanation
Indices: 25726--25766 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25716 GTAAAAAAAG
25726 AAATAAAAATAATAATAATA
1 AAATAAAAATAATAATAATA
*
25746 AAATAATAATAATAATAATA
1 AAATAAAAATAATAATAATA
25766 A
1 A
25767 CAACAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAAAAATAATAATAATA
Found at i:26414 original size:41 final size:41
Alignment explanation
Indices: 26347--26426 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
26337 CTTGTGAAAA
* *
26347 CATCCTGCCCGAAAGTCTTATAGATGGCTCGAAGAACTTAT
1 CATCCTGCCCGAAAGGCTTATAGATGGCCCGAAGAACTTAT
* * *
26388 CATCTTGCTCGAAAGGCTTACT-GATGGCCCGAAGGACTT
1 CATCCTGCCCGAAAGGCTTA-TAGATGGCCCGAAGAACTT
26427 GCCAATTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 32 0.97
42 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (41 bp):
CATCCTGCCCGAAAGGCTTATAGATGGCCCGAAGAACTTAT
Found at i:26623 original size:218 final size:214
Alignment explanation
Indices: 26231--26625 Score: 558
Period size: 218 Copynumber: 1.8 Consensus size: 214
26221 CCCAAAGAAC
** *
26231 TTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTAAAAAACAATTTTCAGAAAATATTTA
1 TTACTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTAAAAAACAATTTTCAGAAAAGATTTA
* *
26296 AATAAAAACCTTTGGAAACCACTTTCTCATTTTTCGAAAATCTTGTGAAAACATCCTGCCCGAAA
66 AATAAAAACCTTTAGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAA
* * * *
26361 GTCTTATAGATGGCTCGAAGAACTTATCATCTTGCTCGAAAGGCTTACTGATGGCCCGAAGGACT
131 GTCTTATAGATGACCCGAAGAACTTATCATATTGCTCAAAAGGCTTACTGATGGCCCGAAGGACT
26426 TGCCAATTTTGGAAATAGT
196 TGCCAATTTTGGAAATAGT
* * * *
26445 TTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCACTTTTCATAAAAGA
1 TTACTAAGTAAGAAACTTTGGAAATCACTTTCTTAC-TTT-AAAAA--ACAATTTTCAGAAAAGA
* * * *
26510 TTTAAATGAGAGA-CTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAATATCCTGCC
62 TTTAAAT-AAAAACCTTTAGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCC
* * *
26574 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATATTGCTCAAAAGGCTTA
126 CGAAAGTCTTATAGATGACCCGAAGAACTTATCATATTGCTCAAAAGGCTTA
26626 TATATGACCC
Statistics
Matches: 156, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
214 33 0.21
215 3 0.02
216 5 0.03
218 112 0.72
219 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (214 bp):
TTACTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTAAAAAACAATTTTCAGAAAAGATTTA
AATAAAAACCTTTAGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAA
GTCTTATAGATGACCCGAAGAACTTATCATATTGCTCAAAAGGCTTACTGATGGCCCGAAGGACT
TGCCAATTTTGGAAATAGT
Found at i:26889 original size:260 final size:260
Alignment explanation
Indices: 26393--26947 Score: 840
Period size: 260 Copynumber: 2.1 Consensus size: 260
26383 CTTATCATCT
* * * * *
26393 TGCTCGAAAGGCTTACTGATGGCCCGAAGGACTTGCCAATTTTGGAAATAGTTTACTAGGTAAGA
1 TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGCAAGA
* * * *
26458 AACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCACTTTTCATAAAAGATTTAAATGAGAGA
66 AAATTTGGAAATCACTTTCTTACTTTTCAAAAATTTAACTTTTCATAAAAGATTTAAATAAGAAA
* * *
26523 CTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAATATCCTGCCCGAAGGTCTTATGG
131 CTTTAGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCGAAGGTCTTATGG
* *
26588 ATGACCCGAAGGACTTATCATATTGCTCAAAAGGCTTATATATGACCCGAAGGATTTAACCACCA
196 ATGACCCGAAGAACTTATCATATTGCTCAAAAGGCTTATATATGACCCAAAGGATTTAACCACCA
* * *
26653 TGCTCAAAAGACTTACGGATGGCCCAAATGACTTACCAACTTTGGAAATAGTTTACTAGGCAAGA
1 TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGCAAGA
* *
26718 AAATTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAACTTTTTATAAAAGATTTAAATAAGAAA
66 AAATTTGGAAATCACTTTCTTACTTTTCAAAAATTTAACTTTTCATAAAAGATTTAAATAAGAAA
* * * *
26783 CTTTGGAAACCACTTTCTCATTTTTCGAAAATCATGTGGAAACATCATGTCTGAAGGTCTTATGG
131 CTTTAGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCGAAGGTCTTATGG
* * * * * * *
26848 ATGGCCTGAAGAACTTATCATCTTGCTCGAAAGGTTTATATATGACCCAAAGGATTTAAGCATCA
196 ATGACCCGAAGAACTTATCATATTGCTCAAAAGGCTTATATATGACCCAAAGGATTTAACCACCA
26913 TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
1 TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
26948 TCACCTTGCT
Statistics
Matches: 262, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
260 262 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (260 bp):
TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGCAAGA
AAATTTGGAAATCACTTTCTTACTTTTCAAAAATTTAACTTTTCATAAAAGATTTAAATAAGAAA
CTTTAGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCGAAGGTCTTATGG
ATGACCCGAAGAACTTATCATATTGCTCAAAAGGCTTATATATGACCCAAAGGATTTAACCACCA
Found at i:26917 original size:42 final size:42
Alignment explanation
Indices: 26864--27005 Score: 153
Period size: 42 Copynumber: 3.4 Consensus size: 42
26854 TGAAGAACTT
* *
26864 ATCATCTTGCTCGAAAGGTTTATATATGACCCAAAGGATTTA
1 ATCATCATGCTCGAAAGGTTTATAGATGACCCAAAGGATTTA
* ** * *
26906 AGCATCATGCTCGAAAGACTTACT-GATGGCCCAAAGGACTT-
1 ATCATCATGCTCGAAAGGTTTA-TAGATGACCCAAAGGATTTA
* * * * *
26947 ATCACCTTGCTCGAAAAGTTTGTAGATGACCCAAATGATTTA
1 ATCATCATGCTCGAAAGGTTTATAGATGACCCAAAGGATTTA
26989 ATCATCATGCTCGAAAG
1 ATCATCATGCTCGAAAG
27006 ACTTACTAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
40 1 0.01
41 29 0.38
42 46 0.60
43 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGGTTTATAGATGACCCAAAGGATTTA
Found at i:27030 original size:83 final size:83
Alignment explanation
Indices: 26855--27030 Score: 253
Period size: 83 Copynumber: 2.1 Consensus size: 83
26845 TGGATGGCCT
* * *
26855 GAAGAACTTATCATCTTGCTCGAAAGGTTTATATATGACCCAAAGGATTTAAGCATCATGCTCGA
1 GAAGAACTTATCACCTTGCTCGAAAAGTTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGA
* **
26920 AAGACTTACTGATGGCCC
66 AAGACTTACTAATAACCC
* * * * *
26938 AAAGGACTTATCACCTTGCTCGAAAAGTTTGTAGATGACCCAAATGATTTAATCATCATGCTCGA
1 GAAGAACTTATCACCTTGCTCGAAAAGTTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGA
27003 AAGACTTACTAATAACCC
66 AAGACTTACTAATAACCC
27021 GAAGAACTTA
1 GAAGAACTTA
27031 CCAATTTTGG
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (83 bp):
GAAGAACTTATCACCTTGCTCGAAAAGTTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGA
AAGACTTACTAATAACCC
Found at i:27222 original size:343 final size:344
Alignment explanation
Indices: 26587--27291 Score: 995
Period size: 343 Copynumber: 2.1 Consensus size: 344
26577 AGGTCTTATG
* * *
26587 GATGACCCGAAGGACTTATCATATTGCTCAAAAGGCTTATATATGACCCGAAGGATTTAACCACC
1 GATGACCCGAAGGACTTATCACATTGCTCAAAAGGCTTATAGATGACCCAAAGGATTTAACCACC
* **
26652 ATGCTCAAAAGACTTACGGATGGCCCAAATGACTTACCAACTTTGGAAATAGTTTACTAGGCAAG
66 ATGCTCAAAAGACTTACGAATAACCCAAATGACTTACCAACTTTGGAAATAGTTTACTAGGCAAG
* * *
26717 AAAATTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAACTTTTTATAAAAGATTTAAATAAGAA
131 AAAATTTGGAAATCGCCTTCTTACATTTCAAAAATTTAACTTTTTAGAAAAGATTTAAATAAGAA
* **
26782 ACTTTGGAAACCACTTTCTCATTTTTCGAAAATCATGTGGAAACATCATGTCTGAAGGTCTTATG
196 ACTTTGGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGTCCAAAGGTCTTATG
* * * *
26847 GATGGCCTGAAGAACTTATCATCTTGCTCG-AAAGGTTTATATATGACCCAAAGGATTTAAGCAT
261 GATGGCCTAAAGAACTTATCATCTTGCTCGAAAAGGCTTATAGATGACCCAAAGGATTTAAGCAA
26911 CATGCTCGAAAGACTTACT
326 CATGCTCGAAAGACTTACT
* * * * * * * *
26930 GATGGCCCAAAGGACTTATCACCTTGCTCGAAAA-GTTTGTAGATGACCCAAATGATTTAATCAT
1 GATGACCCGAAGGACTTATCACATTGCTC-AAAAGGCTTATAGATGACCCAAAGGATTTAACCAC
* * * * *
26994 CATGCTCGAAAGACTTACTAATAACCCGAA-GAACTTACCAATTTTGGAAATAGTTTACTAGGTA
65 CATGCTCAAAAGACTTACGAATAACCCAAATG-ACTTACCAACTTTGGAAATAGTTTACTAGGCA
* * * *
27058 AGAAACTTTGGAAATCGCCTTCTTACATTTCAAAAATTTCACTTTTTAGAAAATATTTAAATGAG
129 AGAAAATTTGGAAATCGCCTTCTTACATTTCAAAAATTTAACTTTTTAGAAAAGATTTAAATAAG
*** *
27123 AAACTTTGGAAATTGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCTTGTCCAAAGGTCTTA
194 AAACTTTGGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGTCCAAAGGTCTTA
* *
27188 TGGATGGTCC-AAAGAACTTATCATCTTGCTCGAAAAGGCTTATAGATGACCCGAATGATTTAAG
259 TGGATGG-CCTAAAGAACTTATCATCTTGCTCGAAAAGGCTTATAGATGACCCAAAGGATTTAAG
*
27252 CAACATGCTCGAAAGATTTACT
323 CAACATGCTCGAAAGACTTACT
27274 GATGACCCGAAGGACTTA
1 GATGACCCGAAGGACTTA
27292 CCAATTTTGG
Statistics
Matches: 316, Mismatches: 42, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
342 1 0.00
343 246 0.78
344 69 0.22
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (344 bp):
GATGACCCGAAGGACTTATCACATTGCTCAAAAGGCTTATAGATGACCCAAAGGATTTAACCACC
ATGCTCAAAAGACTTACGAATAACCCAAATGACTTACCAACTTTGGAAATAGTTTACTAGGCAAG
AAAATTTGGAAATCGCCTTCTTACATTTCAAAAATTTAACTTTTTAGAAAAGATTTAAATAAGAA
ACTTTGGAAACCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGTCCAAAGGTCTTATG
GATGGCCTAAAGAACTTATCATCTTGCTCGAAAAGGCTTATAGATGACCCAAAGGATTTAAGCAA
CATGCTCGAAAGACTTACT
Found at i:29483 original size:6 final size:5
Alignment explanation
Indices: 29470--29559 Score: 78
Period size: 5 Copynumber: 17.8 Consensus size: 5
29460 ATTGTCTTTC
* *
29470 TTCTT TTCCTT TTCCT TT-TT CTCTT TT-TT TTCTCT TTCTT TTCTT TTCTT
1 TTCTT TT-CTT TTCTT TTCTT TTCTT TTCTT TTCT-T TTCTT TTCTT TTCTT
* * *
29520 TTCTTT TTCTC TTCTT TTTTT TTGTT TCTCTT TT-TT TTCT
1 TTC-TT TTCTT TTCTT TTCTT TTCTT T-TCTT TTCTT TTCT
29560 CAATCTTCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
4 10 0.14
5 40 0.58
6 19 0.28
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:29501 original size:11 final size:11
Alignment explanation
Indices: 29485--29560 Score: 66
Period size: 11 Copynumber: 6.7 Consensus size: 11
29475 TTCCTTTTCC
29485 TTTTTCTCTTT
1 TTTTTCTCTTT
29496 TTTTTCTCTTT
1 TTTTTCTCTTT
*
29507 CTTTTCT-TTT
1 TTTTTCTCTTT
*
29517 CTTTTCT-TTT
1 TTTTTCTCTTT
* *
29527 TCTCTTCTTTTTTT
1 T-T-TT-TCTCTTT
29541 TTGTTTCTCTTT
1 TT-TTTCTCTTT
29553 TTTTTCTC
1 TTTTTCTC
29561 AATCTTCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
10 13 0.24
11 24 0.44
12 9 0.16
13 5 0.09
14 4 0.07
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:29516 original size:27 final size:29
Alignment explanation
Indices: 29486--29581 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 29
29476 TCCTTTTCCT
29486 TTTTCTCTTTTTTTTCTC-T-TTCTTTTC
1 TTTTCTCTTTTTTTTCTCTTCTTCTTTTC
* *
29513 TTTTCT-TTTCTTTTTCTCTTCTTTTTTTT
1 TTTTCTCTTT-TTTTTCTCTTCTTCTTTTC
*
29542 TGTTTCTCTTTTTTTTCTCAATCTTCTTTTTC
1 T-TTTCTCTTTTTTTTCTC-TTCTTC-TTTTC
29574 TTTT-TCTT
1 TTTTCTCTT
29582 CAAATATGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.05
27 14 0.25
28 1 0.02
29 7 0.12
30 17 0.30
31 10 0.18
32 5 0.09
ACGTcount: A:0.02, C:0.20, G:0.01, T:0.77
Consensus pattern (29 bp):
TTTTCTCTTTTTTTTCTCTTCTTCTTTTC
Found at i:29540 original size:40 final size:40
Alignment explanation
Indices: 29470--29559 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
29460 ATTGTCTTTC
29470 TTCTTTTCCTTTTCCTTTTTCTCTTTTTTTTCTCTTTCT-T
1 TTCTTTT-CTTTTCCTTTTTCTCTTTTTTTTCTCTTTCTCT
* *
29510 TTCTTTTCTTTT-CTTTTTCTCTTCTTTTTTTTTGTTTCTCT
1 TTCTTTTCTTTTCCTTTTTCTC-T-TTTTTTTCTCTTTCTCT
*
29551 TTTTTTTCT
1 TTCTTTTCT
29560 CAATCTTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 9 0.20
39 6 0.14
40 20 0.45
41 9 0.20
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (40 bp):
TTCTTTTCTTTTCCTTTTTCTCTTTTTTTTCTCTTTCTCT
Found at i:29581 original size:15 final size:15
Alignment explanation
Indices: 29466--29582 Score: 62
Period size: 15 Copynumber: 7.5 Consensus size: 15
29456 ATCTATTGTC
*
29466 TTTCTTCTTTTCCTT
1 TTTCTTCTTTTTCTT
* *
29481 TTCCTT-TTTCTCTT
1 TTTCTTCTTTTTCTT
* *
29495 TTTTTTCTCTTTC-T
1 TTTCTTCTTTTTCTT
*
29509 TTTCTTTTCTTTTCTTT
1 TTTCTTCT-TTTTC-TT
29526 TTCTCTTCTTTTT-TT
1 TT-TCTTCTTTTTCTT
*
29541 TTGT-TTCTCTTTTTTT
1 TT-TCTTCT-TTTTCTT
29557 TCTCAATCTTCTTTTTCTT
1 T-T---TCTTCTTTTTCTT
29576 TTTCTTC
1 TTTCTTC
29583 AAATATGACT
Statistics
Matches: 77, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
14 21 0.27
15 27 0.35
16 3 0.04
17 8 0.10
18 6 0.08
19 8 0.10
20 4 0.05
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (15 bp):
TTTCTTCTTTTTCTT
Found at i:30569 original size:13 final size:13
Alignment explanation
Indices: 30551--30576 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30541 ATAAGTTCAA
30551 TCACAAAATATTT
1 TCACAAAATATTT
30564 TCACAAAATATTT
1 TCACAAAATATTT
30577 AGGTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TCACAAAATATTT
Found at i:32484 original size:30 final size:30
Alignment explanation
Indices: 32450--32522 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
32440 CCTGAAGGAC
32450 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
32480 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
32510 CTGTCCATAGGTC
1 CTATCCAGAGGTC
32523 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:32546 original size:31 final size:31
Alignment explanation
Indices: 32508--32572 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
32498 GATCCTCGGT
*
32508 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
32539 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
32570 AAC
1 AAC
32573 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:33555 original size:20 final size:22
Alignment explanation
Indices: 33530--33587 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
33520 TTCCCCTTGA
33530 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
33550 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
33573 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
33588 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:33648 original size:64 final size:63
Alignment explanation
Indices: 33564--33715 Score: 182
Period size: 64 Copynumber: 2.4 Consensus size: 63
33554 CATCGATGCA
* * *
33564 TTCTTTAACATGTGCATCGATGCACTACTCATGCATCGATACACAAATTACCTTCGATG-TT-
1 TTCTTTAAAAAGTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTC
* * * * *
33625 TTCATTTAAAAAGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTT
1 TTC-TTTAAAAA-G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTT
33690 C
63 C
*
33691 TTCTTTAAAGAGTGCATCGATGCAC
1 TTCTTTAAAAAGTGCATCGATGCAC
33716 ATTCAATATG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
61 3 0.04
62 6 0.08
63 14 0.18
64 42 0.55
65 9 0.12
66 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (63 bp):
TTCTTTAAAAAGTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTC
Found at i:33731 original size:65 final size:64
Alignment explanation
Indices: 33576--33737 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
33566 CTTTAACATG
* * *
33576 TGCATCGATGCACT-ACTCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTAAAAAGGA
1 TGCATCGATGCACTCAAT-ATGCATCGATACACCAATTACATTCGATGTTTTCATTTAAAAAGGA
** * * *
33640 TGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTC-TTTAAAGA-G
1 TGCATCGATGCACTCAATATGCATCGATACACCAATTACATTCGATG-TT-TTCATTTAAAAAGG
33703 -
64 A
33703 TGCATCGATGCACATTCAATATGCATCGATACACC
1 TGCATCGATGCAC--TCAATATGCATCGATACACC
33738 TTGCCCAGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 13 0.16
64 40 0.48
65 27 0.33
66 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCACTCAATATGCATCGATACACCAATTACATTCGATGTTTTCATTTAAAAAGGA
Found at i:34204 original size:3 final size:3
Alignment explanation
Indices: 34196--34224 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34186 GCTTACGGGG
34196 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
34225 GAAATAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43167 original size:14 final size:14
Alignment explanation
Indices: 43134--43195 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
43124 ATTTTAATGT
* *
43134 TAAAATTTAAAATA
1 TAAACTTTAAATTA
*
43148 TAAAACTTTAAATTC
1 T-AAACTTTAAATTA
* *
43163 TAAACTCTAATTTA
1 TAAACTTTAAATTA
* *
43177 TAAATTTTAAATTT
1 TAAACTTTAAATTA
43191 TAAAC
1 TAAAC
43196 CCAAGACCTT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAACTTTAAATTA
Found at i:51679 original size:23 final size:23
Alignment explanation
Indices: 51651--51701 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
51641 ATTTATAATT
51651 AGATTTTAAAAGATAAAATTATA
1 AGATTTTAAAAGATAAAATTATA
51674 AGATTTTAAAAGATAAAATTATA
1 AGATTTTAAAAGATAAAATTATA
51697 AGATT
1 AGATT
51702 CAGAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (23 bp):
AGATTTTAAAAGATAAAATTATA
Found at i:55474 original size:19 final size:20
Alignment explanation
Indices: 55433--55476 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
55423 ACGACTCTTT
**
55433 TAAAAATAAATTTTAATCTTA
1 TAAAAATAAA-TTTAATAATA
55454 TAAAAATAAA-TTAATAATA
1 TAAAAATAAATTTAATAATA
55473 TAAA
1 TAAA
55477 TGTAACGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAAATTTAATAATA
Found at i:59036 original size:11 final size:11
Alignment explanation
Indices: 59022--59047 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59012 AATTTTAATA
59022 TTTTTTTTTCT
1 TTTTTTTTTCT
59033 TTTTTTTTTCT
1 TTTTTTTTTCT
59044 TTTT
1 TTTT
59048 ATCAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:62359 original size:21 final size:22
Alignment explanation
Indices: 62314--62367 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
62304 GTGAAAAGTC
*
62314 TTTAAAACCCCCATCAATCATT
1 TTTAAAGCCCCCATCAATCATT
62336 TTTAAAGCCCCCATCAATCATT
1 TTTAAAGCCCCCATCAATCATT
*
62358 TTCAAAGCCC
1 TTTAAAGCCC
62368 TTACTGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (22 bp):
TTTAAAGCCCCCATCAATCATT
Found at i:67737 original size:6 final size:6
Alignment explanation
Indices: 67726--67751 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
67716 GCTTTTAAAA
67726 AAAACT AAAACT AAAACT AAAACT AA
1 AAAACT AAAACT AAAACT AAAACT AA
67752 TGGGCCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAACT
Found at i:67806 original size:2 final size:2
Alignment explanation
Indices: 67799--67829 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67789 TACGTAAAAC
67799 AT AT 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 AT AT A
67830 CATTTAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67954 original size:23 final size:23
Alignment explanation
Indices: 67921--68001 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
67911 TAAGACAATT
*
67921 TATATAAAAACATTATATATATA
1 TATATATAAACATTATATATATA
67944 TATATATAAACATTATATATATA
1 TATATATAAACATTATATATATA
* *
67967 TGATAGTA-AAACAATATATTTATA
1 T-ATA-TATAAACATTATATATATA
*
67991 TAGTGTATAAA
1 TA-TATATAAA
68002 AATATTTACA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
23 26 0.52
24 22 0.44
25 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.40
Consensus pattern (23 bp):
TATATATAAACATTATATATATA
Found at i:68129 original size:10 final size:10
Alignment explanation
Indices: 68114--68139 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
68104 TAAAAAATAG
68114 AAAATTAAAA
1 AAAATTAAAA
68124 AAAATTAAAA
1 AAAATTAAAA
68134 AAAATT
1 AAAATT
68140 GTAATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:80268 original size:22 final size:22
Alignment explanation
Indices: 80229--80291 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
80219 GTCTTTATGT
* *
80229 CACGTTTATCTCTGCCTTTGTAG
1 CACGTTT-GCTCTACCTTTGTAG
* *
80252 CACGTTTGCTCTACCTTTTTGG
1 CACGTTTGCTCTACCTTTGTAG
80274 CACGTTTGCTCTACCTTT
1 CACGTTTGCTCTACCTTT
80292 TGGTAGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 29 0.81
23 7 0.19
ACGTcount: A:0.11, C:0.29, G:0.16, T:0.44
Consensus pattern (22 bp):
CACGTTTGCTCTACCTTTGTAG
Found at i:80294 original size:21 final size:22
Alignment explanation
Indices: 80251--80292 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
80241 TGCCTTTGTA
80251 GCACGTTTGCTCTACCTTTTTG
1 GCACGTTTGCTCTACCTTTTTG
80273 GCACGTTTGCTCTACCTTTT
1 GCACGTTTGCTCTACCTTTT
80293 GGTAGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.17, T:0.45
Consensus pattern (22 bp):
GCACGTTTGCTCTACCTTTTTG
Found at i:81019 original size:26 final size:26
Alignment explanation
Indices: 80983--81036 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
80973 GAGCCCAAAT
80983 GTTTTGGTATAAACCCATAAAACACA
1 GTTTTGGTATAAACCCATAAAACACA
81009 GTTTTGGTATAAACCCATAAAACACA
1 GTTTTGGTATAAACCCATAAAACACA
81035 GT
1 GT
81037 CTTCTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (26 bp):
GTTTTGGTATAAACCCATAAAACACA
Found at i:82984 original size:3 final size:3
Alignment explanation
Indices: 82976--83039 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
82966 GTTGAAGAAT
82976 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
83024 AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
83040 ACACTTAATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:83616 original size:19 final size:18
Alignment explanation
Indices: 83578--83639 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
83568 TTTAAGGTTC
83578 TATA-ATTTAAT--TATT
1 TATATATTTAATCATATT
* * *
83593 CATATATTTGTATTATATT
1 TATATATTT-AATCATATT
83612 TATATATTTAATCATATT
1 TATATATTTAATCATATT
83630 TAATATATTT
1 T-ATATATTT
83640 TATATGTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 2 0.05
18 8 0.22
19 20 0.54
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATATTTAATCATATT
Found at i:83639 original size:9 final size:9
Alignment explanation
Indices: 83606--83644 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
83596 ATATTTGTAT
83606 TATATTT-A
1 TATATTTAA
83614 TATATTTAA
1 TATATTTAA
83623 TCATATTTAA
1 T-ATATTTAA
*
83633 TATATTTTA
1 TATATTTAA
83642 TAT
1 TAT
83645 GTAAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.25
9 12 0.43
10 9 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATTTAA
Found at i:84736 original size:156 final size:156
Alignment explanation
Indices: 84549--84868 Score: 622
Period size: 156 Copynumber: 2.1 Consensus size: 156
84539 ATTTAGACCC
84549 TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
1 TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
*
84614 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAATTATTCTTATGATCATTTCTTTA
66 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAACTATTCTTATGATCATTTCTTTA
84679 TTTTATTACTATGTCTTATAATCGTA
131 TTTTATTACTATGTCTTATAATCGTA
*
84705 TATATATAATTATTACGTTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
1 TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
84770 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAACTATTCTTATGATCATTTCTTTA
66 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAACTATTCTTATGATCATTTCTTTA
84835 TTTTATTACTATGTCTTATAATCGTA
131 TTTTATTACTATGTCTTATAATCGTA
84861 TATATATA
1 TATATATA
84869 TATATATTTC
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 162 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.57
Consensus pattern (156 bp):
TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAACTATTCTTATGATCATTTCTTTA
TTTTATTACTATGTCTTATAATCGTA
Found at i:84954 original size:30 final size:31
Alignment explanation
Indices: 84915--84986 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
84905 TATTATTTTA
* *
84915 TTTTATTTACCT-T-TATATCTATACATTATC
1 TTTTTTTTACCTCTATATATATATA-ATTATC
*
84945 TTTTTTTTACCTCTATATATATATAATTATT
1 TTTTTTTTACCTCTATATATATATAATTATC
84976 TTTGTTTTTAC
1 TTT-TTTTTAC
84987 TATTACTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.31
31 9 0.25
32 16 0.44
ACGTcount: A:0.25, C:0.12, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTTTTTACCTCTATATATATATAATTATC
Found at i:84978 original size:28 final size:27
Alignment explanation
Indices: 84912--84978 Score: 64
Period size: 31 Copynumber: 2.3 Consensus size: 27
84902 TTATATTATT
*
84912 TTATTTTATTTACCTTTATATCTATACA
1 TTATTTT-TTTACCTTTATATATATACA
84940 TTATCTTTTTTTTACCTCTATATATATATA-A
1 TTA---TTTTTTTACCT-T-TATATATATACA
84971 TTATTTTT
1 TTATTTTT
84979 GTTTTTACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
28 8 0.24
30 7 0.21
31 9 0.27
32 9 0.27
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATTTTTTTACCTTTATATATATACA
Done.