Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001951.1 Hibiscus syriacus cultivar Beakdansim tig00003947_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: 83317
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:189 original size:10 final size:10
Alignment explanation
Indices: 183--211 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
173 GTAAATAGAG
183 ATAAATAAAA
1 ATAAATAAAA
193 ATAAATAAAA
1 ATAAATAAAA
203 ATAAATAAA
1 ATAAATAAA
212 TGGTAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:1597 original size:2 final size:2
Alignment explanation
Indices: 1586--1633 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
1576 AAGGGGCCCG
1586 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1627 TCA TA TA
1 T-A TA TA
1634 AGATTTGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4271 original size:30 final size:30
Alignment explanation
Indices: 4208--4313 Score: 151
Period size: 30 Copynumber: 3.5 Consensus size: 30
4198 GATGGCCTTG
* * *
4208 GTCCCTGTACTATTTAACA-TGAGTGGTCAA
1 GTCCCTGTACTATTTGACATTG-GTGGCCCA
* *
4238 GTCCTTATACTATTTGACATTGGTGGCCCA
1 GTCCCTGTACTATTTGACATTGGTGGCCCA
4268 GTCCCTGTACTATTTGACATTGGTGGCCCA
1 GTCCCTGTACTATTTGACATTGGTGGCCCA
4298 GTCCCTGTACTATTTG
1 GTCCCTGTACTATTTG
4314 GTGCTTAACT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 66 0.97
31 2 0.03
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (30 bp):
GTCCCTGTACTATTTGACATTGGTGGCCCA
Found at i:4702 original size:25 final size:24
Alignment explanation
Indices: 4660--4736 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 24
4650 AAAAATTGAT
4660 GAAGAAGTTTTAAAAATGGTTT-ATG
1 GAAGAA-TTTTAAAAAT-GTTTAATG
4685 GAAGAATTTTAAATAATGTTTAATG
1 GAAGAATTTTAAA-AATGTTTAATG
* *
4710 AAAGAATTTTGAAAAATGTTTGATG
1 GAAGAATTTT-AAAAATGTTTAATG
4735 GA
1 GA
4737 CATGAGCTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 11 0.24
25 32 0.70
26 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (24 bp):
GAAGAATTTTAAAAATGTTTAATG
Found at i:4907 original size:25 final size:23
Alignment explanation
Indices: 4860--4929 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 23
4850 ATTGATGAAG
*
4860 TTTTAAAAATGGTTTATGGAAGAA
1 TTTTAAAAAT-GTTTATGAAAGAA
4884 TTTTAAATAATGTTTAATGAAAGAA
1 TTTTAAA-AATGTTT-ATGAAAGAA
4909 TTTTGAAAAATGTTTGATGAA
1 TTTT-AAAAATGTTT-ATGAA
4930 GTTTTTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
24 11 0.27
25 27 0.66
26 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (23 bp):
TTTTAAAAATGTTTATGAAAGAA
Found at i:5553 original size:2 final size:2
Alignment explanation
Indices: 5546--5587 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5536 AAATTTATTG
5546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5588 ATTACATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8184 original size:18 final size:19
Alignment explanation
Indices: 8157--8198 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
8147 AATAATTTTT
8157 AAAATAA-TTTTAAGAAAA
1 AAAATAATTTTTAAGAAAA
* *
8175 AAAATCATTTTTAAGACAA
1 AAAATAATTTTTAAGAAAA
8194 AAAAT
1 AAAAT
8199 TAGTATGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATAATTTTTAAGAAAA
Found at i:9464 original size:13 final size:13
Alignment explanation
Indices: 9446--9480 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
9436 ATTTTCTTCT
9446 CCTCTCTATGCTC
1 CCTCTCTATGCTC
9459 CCTCTCTATGCTC
1 CCTCTCTATGCTC
9472 CCTCTCTAT
1 CCTCTCTAT
9481 TTCCAGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.46, G:0.06, T:0.40
Consensus pattern (13 bp):
CCTCTCTATGCTC
Found at i:13120 original size:2 final size:2
Alignment explanation
Indices: 13113--13142 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13103 TTCGCCACAT
*
13113 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13143 GTTTGCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13284 original size:38 final size:37
Alignment explanation
Indices: 13169--13349 Score: 185
Period size: 37 Copynumber: 4.9 Consensus size: 37
13159 TAAAATTACG
* * * *
13169 TATATAATATGTAGTTTTCAAAACATTTTTGAAAAAA
1 TATATAATATATAATTTTTAAAACATTTTTGAAAATA
* ** *
13206 TATATATTATATGGTTTTTAAAACATTTTTAAAAAT-
1 TATATAATATATAATTTTTAAAACATTTTTGAAAATA
13242 TATATAATATATAAATTTTTAAAACATTTTTGAAAATA
1 TATATAATATAT-AATTTTTAAAACATTTTTGAAAATA
13280 TATATAATATATAATTTTTGAAAAAACATTTTT-AAAA-A
1 TATATAATATATAATTTTT---AAAACATTTTTGAAAATA
* * *
13318 CATAT-A-ATAT-AGTTTTAAGACATTTTTGAAAA
1 TATATAATATATAATTTTTAAAACATTTTTGAAAA
13350 GAGAAAATAA
Statistics
Matches: 125, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
32 10 0.08
33 4 0.03
35 5 0.04
36 15 0.12
37 59 0.47
38 17 0.14
39 4 0.03
40 11 0.09
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAACATTTTTGAAAATA
Found at i:13584 original size:20 final size:20
Alignment explanation
Indices: 13559--13651 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
13549 TTTTCCCAAT
13559 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
13579 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
13599 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
13620 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
13641 TCGCAATGCGA
1 TCGCAATGCGA
13652 TAATGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:13601 original size:41 final size:41
Alignment explanation
Indices: 13556--13651 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
13546 TGATTTTCCC
13556 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
13597 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
13638 AAATCGCAATGCGA
1 AATTCGCAATGCGA
13652 TAATGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:13605 original size:21 final size:20
Alignment explanation
Indices: 13559--13671 Score: 102
Period size: 20 Copynumber: 5.5 Consensus size: 20
13549 TTTTCCCAAT
*
13559 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
13579 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
13599 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
13620 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
* *
13641 TCGCAATGCG-ATAATGACTA
1 TCGCAATGCGAATAAGGA-AA
13661 TCGCAATGCGA
1 TCGCAATGCGA
13672 TAATAAAAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.01
20 43 0.60
21 28 0.39
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:13682 original size:41 final size:41
Alignment explanation
Indices: 13637--13714 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
13627 GCGAATTGGG
* * *
13637 AAAATCGCAATGCGATAATGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATAATGACTATCGCAACGCGATAATAA
* * *
13678 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATAATGACTATCGCAACGCGATA
13715 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATAATGACTATCGCAACGCGATAATAA
Found at i:13730 original size:20 final size:20
Alignment explanation
Indices: 13682--13733 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
13672 TAATAAAAAA
* *
13682 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
13702 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
13722 TCGCAACGCGAT
1 TCGCAACGCGAT
13734 TTACTTAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:14317 original size:19 final size:19
Alignment explanation
Indices: 14289--14333 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
14279 GCAACGAGAT
* *
14289 AATCGTAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
14308 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
14327 AATCGCA
1 AATCGCA
14334 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:14351 original size:19 final size:19
Alignment explanation
Indices: 14329--14532 Score: 203
Period size: 19 Copynumber: 11.1 Consensus size: 19
14319 GAAACCAAAA
*
14329 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
14348 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
14367 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
14386 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
14405 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
14425 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
14441 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
14458 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
14472 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
14491 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
14511 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
14531 TC
1 TC
14533 AACCAAAAGA
Statistics
Matches: 157, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
14 20 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 79 0.50
20 49 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:14448 original size:39 final size:38
Alignment explanation
Indices: 14334--14532 Score: 170
Period size: 33 Copynumber: 5.4 Consensus size: 38
14324 CAAAATCGCA
*
14334 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGC-G
1 TTGCGATTTTCATTTCGCGTTGCGATTTTC-TTTCGCGG
*
14372 TTGCGATTTTCATTTCGCGTTGCGATTTTAATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTT-CTTTCGCGG
*
14411 TTGCGATTTTCATTTCGCGTTGCGATTGTC--T---GG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
* ** *
14444 TCGCGATAGTCATTTCGCGTTGCGA--TTC--TCTC-G
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
** * *
14477 TTGCGATAGTCATTTCCGCGTTGCGATTCTCATTATCTC-G
1 TTGCGATTTTCATTT-CGCGTTGCGATTTTC-TT-TCGCGG
14517 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
14533 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 12, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
31 3 0.02
33 39 0.28
34 10 0.07
36 3 0.02
38 34 0.25
39 30 0.22
40 18 0.13
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
Found at i:14509 original size:20 final size:20
Alignment explanation
Indices: 14475--14532 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
14465 GCGATTCTCT
**
14475 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
14495 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
14515 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
14533 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:16613 original size:21 final size:21
Alignment explanation
Indices: 16589--16655 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16579 TCATTCCTCG
16589 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
16610 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
16631 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
16652 AGAG
1 AGAG
16656 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:16613 original size:42 final size:42
Alignment explanation
Indices: 16533--16655 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
16523 GCCCGACTCG
* * * * ** *
16533 CCTATCATCCCTCAAGAGTCCACTCCTATTGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
16575 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
16617 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
16656 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:18033 original size:14 final size:14
Alignment explanation
Indices: 18014--18049 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
18004 ATTGTTTAAT
18014 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
18028 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
18042 TGATTTGT
1 TGATTTGT
18050 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:18250 original size:19 final size:19
Alignment explanation
Indices: 18228--18345 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
18218 CGAAATTAAA
18228 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
18247 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
18262 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
18280 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
18295 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
18313 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
18332 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
18346 GGACATTAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:18274 original size:33 final size:33
Alignment explanation
Indices: 18232--18325 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
18222 ATTAAATTCG
18232 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
18265 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
18298 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
18326 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:20629 original size:12 final size:12
Alignment explanation
Indices: 20612--20636 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20602 TCTTCGGGGA
20612 CTTTTTCTTCTT
1 CTTTTTCTTCTT
20624 CTTTTTCTTCTT
1 CTTTTTCTTCTT
20636 C
1 C
20637 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:22133 original size:14 final size:14
Alignment explanation
Indices: 22114--22150 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22104 CATCAATTAA
22114 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
22128 ACAAATCATCTTTT
1 ACAAATCAACATTT
22142 ACAAATCAA
1 ACAAATCAA
22151 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:24023 original size:20 final size:20
Alignment explanation
Indices: 23998--24050 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
23988 TAGTTTACTT
23998 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAACTTAAAA
24018 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAACTTAAAA
24038 TCGCAACACGAAA
1 TCGCAACACGAAA
24051 ATGACTATCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.13
Consensus pattern (20 bp):
TCGCAACACGAAACTTAAAA
Found at i:24060 original size:20 final size:20
Alignment explanation
Indices: 23998--24064 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
23988 TAGTTTACTT
* *
23998 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGAAAA
* *
24018 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGAAAA
**
24038 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGAAAA
24058 TCGCAAC
1 TCGCAAC
24065 GCGGAAATGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:24072 original size:20 final size:20
Alignment explanation
Indices: 23998--24083 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 20
23988 TAGTTTACTT
* * **
23998 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
* * **
24018 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
24038 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
24058 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
24078 TCGCAA
1 TCGCAA
24084 TGTGAAATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:24112 original size:14 final size:14
Alignment explanation
Indices: 24093--24149 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
24083 ATGTGAAATG
24093 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
24107 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
24123 ATAAATCGCAACGAC
1 A-AAATCGCAACGAC
24138 AAAATCGCAACG
1 AAAATCGCAACG
24150 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 21 0.55
15 4 0.11
16 4 0.11
17 9 0.24
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24132 original size:31 final size:31
Alignment explanation
Indices: 24094--24154 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
24084 TGTGAAATGA
24094 AAATCGCAACGACAAAATCGCAACGCGAAAT
1 AAATCGCAACGACAAAATCGCAACGCGAAAT
24125 AAATCGCAACGACAAAATCGCAACGCGAAA
1 AAATCGCAACGACAAAATCGCAACGCGAAA
24155 CACAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.08
Consensus pattern (31 bp):
AAATCGCAACGACAAAATCGCAACGCGAAAT
Found at i:24183 original size:19 final size:17
Alignment explanation
Indices: 24161--24256 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
24151 GAAACACAAA
24161 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
24180 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
24196 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
24212 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
24228 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
24245 TCGCATTGCGAT
1 TCGC-TTGCGAT
24257 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:24202 original size:14 final size:14
Alignment explanation
Indices: 24183--24240 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
24173 TTTCATTTCG
24183 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
24197 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
24213 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
24229 CGTTGCGATTTT
1 CGTTGCGATTTT
24241 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:24247 original size:33 final size:33
Alignment explanation
Indices: 24166--24256 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
24156 ACAAATCGCA
24166 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
24199 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
24231 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
24257 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:24263 original size:19 final size:20
Alignment explanation
Indices: 24241--24284 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
24231 TTGCGATTTT
24241 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
24260 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
24280 CATTT
1 CATTT
24285 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:24292 original size:20 final size:20
Alignment explanation
Indices: 24250--24295 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24240 TCATTTCGCA
*
24250 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
24270 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
24290 TTGCGA
1 TTGCGA
24296 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:24793 original size:18 final size:18
Alignment explanation
Indices: 24767--24811 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
24757 GTCGATCAGA
*
24767 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
24785 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
24803 TGATGGCTC
1 TGATGGCTC
24812 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:26154 original size:20 final size:20
Alignment explanation
Indices: 26129--26166 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26119 AATAGTTTCT
26129 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
26149 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
26167 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:26455 original size:22 final size:22
Alignment explanation
Indices: 26430--26473 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
26420 GATTTAGATA
26430 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
26452 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
26474 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:26686 original size:20 final size:20
Alignment explanation
Indices: 26661--26713 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
26651 GATTATGTAT
*
26661 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
26681 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
26701 TATCTCGTTGCGA
1 TATCGCGTTGCGA
26714 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:26726 original size:41 final size:41
Alignment explanation
Indices: 26681--26758 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
26671 CGAAAGTCAG
* * *
26681 TATCGCGTTGCGAA-AGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGC-AATAGTAAGTATCGCATTGCGATTTTTTAT
*
26722 TATCGCATTGCAATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCAATAGTAAGTATCGCATTGCGATTTT
26759 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.06
41 30 0.94
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCAATAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:26788 original size:20 final size:20
Alignment explanation
Indices: 26744--26836 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
26734 ATAGTCAGTA
* **
26744 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
26765 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
26785 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
26806 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
26826 TCGCATTGCGA
1 TCGCATTGCGA
26837 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:26789 original size:41 final size:41
Alignment explanation
Indices: 26744--26839 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
26734 ATAGTCAGTA
*
26744 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
26785 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
26826 TCGCATTGCGAATT
1 TCGCATTGCGAATT
26840 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:27110 original size:36 final size:37
Alignment explanation
Indices: 27056--27159 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 37
27046 TTTTGAAAAC
*
27056 TATATAACATATAG-TTTAAAAACATTTTTTAAAAT-
1 TATATAATATATAGTTTTAAAAACATTTTTTAAAATG
* * *
27091 TTTATAATATAT-GATTTTAAAAAAATATTTTTGAAATG
1 TATATAATATATAG-TTTTAAAAACAT-TTTTTAAAATG
*
27129 TATATTATATATAGTTTT-AAAACAATTTTTT
1 TATATAATATATAGTTTTAAAAAC-ATTTTTT
27160 TAGTATATGT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
34 1 0.02
35 10 0.18
36 10 0.18
37 18 0.32
38 16 0.29
39 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAACATTTTTTAAAATG
Found at i:27121 original size:38 final size:39
Alignment explanation
Indices: 27056--27161 Score: 100
Period size: 38 Copynumber: 2.9 Consensus size: 39
27046 TTTTGAAAAC
* *
27056 TATATAACATATAG-TTT--AAAAACATTTTTTAAAAT-
1 TATATAATATATAGTTTTAAAAAAATATTTTTTAAAATG
* *
27091 TTTATAATATAT-GATTTTAAAAAAATA-TTTTTGAAATG
1 TATATAATATATAG-TTTTAAAAAAATATTTTTTAAAATG
* *
27129 TATATTATATATAGTTTTAAAACAAT-TTTTTTA
1 TATATAATATATAGTTTTAAAAAAATATTTTTTA
27162 GTATATGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
34 1 0.02
35 10 0.18
36 3 0.05
37 9 0.16
38 32 0.57
39 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (39 bp):
TATATAATATATAGTTTTAAAAAAATATTTTTTAAAATG
Found at i:27199 original size:17 final size:17
Alignment explanation
Indices: 27177--27209 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27167 TGTTATATAG
*
27177 TTTTTATTTATTATTTA
1 TTTTTATTCATTATTTA
27194 TTTTTATTCATTATTT
1 TTTTTATTCATTATTT
27210 TTATTCACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTCATTATTTA
Found at i:27201 original size:13 final size:13
Alignment explanation
Indices: 27191--27216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27181 TATTTATTAT
27191 TTATTTTTATTCA
1 TTATTTTTATTCA
27204 TTATTTTTATTCA
1 TTATTTTTATTCA
27217 CTCGTTGTCA
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTTATTCA
Found at i:28245 original size:19 final size:18
Alignment explanation
Indices: 28223--28262 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
28213 TTTTTTTTTC
28223 TTTTAATTTCTTATATATG
1 TTTTAATTTCTT-TATATG
*
28242 TTTTAATTTCTTTTTATG
1 TTTTAATTTCTTTATATG
28260 TTT
1 TTT
28263 ATATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTAATTTCTTTATATG
Found at i:28381 original size:22 final size:21
Alignment explanation
Indices: 28353--28404 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
28343 ATATTTTTAT
*
28353 TTTTATTTGTCTATTTTATTTG
1 TTTTATTTGTC-ATTTGATTTG
* *
28375 TTTTATTTTTCCTTTGATTTG
1 TTTTATTTGTCATTTGATTTG
28396 TCTTTATTT
1 T-TTTATTT
28405 TTTTATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (21 bp):
TTTTATTTGTCATTTGATTTG
Found at i:28472 original size:4 final size:4
Alignment explanation
Indices: 28465--28493 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28455 TTCTATTTAG
28465 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
28494 CCTCTAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:33174 original size:81 final size:82
Alignment explanation
Indices: 33024--33407 Score: 413
Period size: 81 Copynumber: 4.7 Consensus size: 82
33014 TTTGCTAACT
* *
33024 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGTATAGCTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
33088 AGAAGGGTTATCTGCC-
66 AGAAGGGTTATCTGCCA
* * * * * *
33104 AAAGACCATCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTTC
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAG-TC
33169 -AGAAGGGTTATCTGCCA
65 GAGAAGGGTTATCTGCCA
* * * *
33186 ACTGAAGACCTTCGAGTTCGACTACGTTCAGC-TCCAAGGCACGTCATTTGCAGTATAGCTTAAG
1 A---AAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAG
*
33250 TCGAGAAGGGCTATCTGCC-
63 TCGAGAAGGGTTATCTGCCA
* * * ** * * * *
33269 AAAGACCCTT-AAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGC
1 AAAGA-CCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
33333 TAGAAGGGTTATTTGTGACCA
65 GAGAAGGGTTA--TCTG-CCA
* *
33354 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACGTCATTTGCAACATA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATA
33408 GTTGATAACT
Statistics
Matches: 246, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
80 45 0.18
81 81 0.33
82 3 0.01
83 6 0.02
84 66 0.27
85 45 0.18
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (82 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGCCA
Found at i:33253 original size:165 final size:165
Alignment explanation
Indices: 32995--33402 Score: 611
Period size: 165 Copynumber: 2.5 Consensus size: 165
32985 TGCAATATAT
* * * *
32995 CTCAAGACAAGAAGGGCTATTTGCTAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATTTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
33060 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCATCGAGTTCGATTA
66 CACGTCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCATCAAGTTCGATTA
* *
33125 CACTCAGCTTCGAGGGCATATCATTTGCAGCATAA
131 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * * *
33160 CTTAA-GTTCAGAAGGGTTATCTGCCAACTGAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAG
1 CTCAAGGCT-AGAAGGGTTATTTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
* *
33224 GCACGTCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATT
65 GCACGTCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCATCAAGTTCGATT
*
33289 ACACTCAGCTTTGAGGGCACATCATTTACAGCATAA
130 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
** * *
33325 CTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATTTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
33390 CACGTCATTTGCA
66 CACGTCATTTGCA
33403 ACATAGTTGA
Statistics
Matches: 215, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
165 213 0.99
166 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (165 bp):
CTCAAGGCTAGAAGGGTTATTTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
CACGTCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCATCAAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:34265 original size:24 final size:24
Alignment explanation
Indices: 34238--34287 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
34228 TGGTGGTTGA
34238 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
34262 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
34286 TT
1 TT
34288 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:35653 original size:165 final size:164
Alignment explanation
Indices: 35115--36127 Score: 1456
Period size: 165 Copynumber: 6.2 Consensus size: 164
35105 CACGCGAACA
* * *
35115 ATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTTAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* *
35180 GCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTC
66 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACC-AAAGACCTTCGAGTTC
35245 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
130 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
* * * * * *
35280 ATAGATTAAATCGATAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTGCACTCAACTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* * * *
35345 GCACATCATTTATAGCATAACTCAGGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTAG
66 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCG
*
35410 ACTACGCTCAGCTCCAAGGCACGTCATTTGCAGC
131 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
* * *
35444 ATAACTTAAGTCGAGAAGTGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* *
35509 GTACATCATTTACAGCATAACTCAAGGCTAGATGGGTTATCTGTAACCAAAAGACCTTCGAGTTC
66 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACC-AAAGACCTTCGAGTTC
35574 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
130 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
* * * *
35609 ATAGCTTAAGTTGAGAAGGGCTATCTGCCAATGACCCCCGAGTTTGATTACACTCAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* * * *
35674 GCATATCATTTACAGCATAACTCAGGGCTAGAAGGGTTATCTGTAACCAAATACCTTTGAGTTCG
66 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCG
*
35739 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGT
131 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
* * *
35773 ATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAG-CTCTCGAGTTCGATTACACTCAACTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* * * * * * * *
35837 GAACATAATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGACCTTTGAGTT
66 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT--AACCAAAGACCTTCGAGTT
*
35901 CGACTACGCTCAGCTCCAAGGCACATCATTTGCAGA
129 CGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
* *
35937 ATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCTTCGAGG
1 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* * * * *
36002 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGACCTCCGAGTT
66 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT--AACCAAAGACCTTCGAGTT
* *
36066 CGACTACGCTCAGCTCCAAGGCACATCATTTACAGA
129 CGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
** * *
36102 ATAGCCCAAGGCAAGAAGGGCTATCT
1 ATAGCTTAAGTCGAGAAGGGCTATCT
36128 ATCAATAAAA
Statistics
Matches: 768, Mismatches: 76, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
162 1 0.00
163 60 0.08
164 310 0.40
165 397 0.52
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (164 bp):
ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCG
ACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
Found at i:35717 original size:329 final size:329
Alignment explanation
Indices: 35119--36096 Score: 1496
Period size: 329 Copynumber: 3.0 Consensus size: 329
35109 CGAACAATAG
* * *
35119 CTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTTAGCTTCGAGGGCAC
1 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGAAC
* *
35184 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
66 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACT
* *
35249 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGATTAAATCGATAAGGGCTATCTGCCAAAGA
131 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGA
* * *
35314 CCCCCGAGTTCGATTGCACTCAACTTCGAGGGCACATCATTTATAGCATAACTCAGGGCTAGAAG
196 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAGGGCTAGAAG
* *
35379 GGTTATCTGTAACCAAAGACCTTTGAGTTAGACTACGCTCAGCTCCAAGGCACGTCATTTGCAGC
261 GGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
35444 ATAA
326 ATAA
* *
35448 CTTAAGTCGAGAAGTGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGTAC
1 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGAAC
*
35513 ATCATTTACAGCATAACTCAAGGCTAGATGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACT
66 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACT
* * *
35578 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAATGA
131 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGA
* *
35643 CCCCCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAGGGCTAGAAG
196 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAGGGCTAGAAG
* *
35708 GGTTATCTGTAACCAAATACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGT
261 GGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
*
35773 ATAG
326 ATAA
* * * *
35777 CTTAAGTCGAGAAGGGTTATCTGCCAAAG-CTCTCGAGTTCGATTACACTCAACTTCGAGGGAAC
1 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGAAC
* * * * * * *
35841 ATAATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCT-TCCAACC-AAAGACCTTTGAGTTCGA
66 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT--AACCAAAAGACCTTCGAGTTCGA
*
35904 CTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGATAAGGGCTATCTGCCAAA
129 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAA
* * * * * * *
35969 GACTCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGA
194 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAGGGCTAGA
**
36034 AGGGTTATCT-TCCAACCAAAGACCTCCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
259 AGGGTTATCTGT--AACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
36097 ACAGAATAGC
Statistics
Matches: 593, Mismatches: 52, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
327 2 0.00
328 206 0.35
329 385 0.65
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (329 bp):
CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGAAC
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGA
CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAGGGCTAGAAG
GGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
ATAA
Found at i:36606 original size:2 final size:2
Alignment explanation
Indices: 36599--36638 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
36589 GTCCACATTT
* *
36599 TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36639 GTTTGCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36712 original size:36 final size:36
Alignment explanation
Indices: 36665--36944 Score: 256
Period size: 35 Copynumber: 7.8 Consensus size: 36
36655 TGAAAATACG
*
36665 TATATAATATATAGTTTTCAAAACATTTTTGAAAAA
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAA
* *
36701 TATATATTATATAGTTTTTAAAACATTTTT-AAAAA
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAA
* * * *
36736 T-TAT-ATATATAATTTTTAAAATAATTTTGAAAATA
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAA-A
*
36771 TATATAATATATAATTTTTGAAAAAACATTTTT-AAAAA
1 TATATAATATAT-AGTTTT--AAAAACATTTTTGAAAAA
* *
36809 CATAT-A-ATATAGTTTT-AAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAA
* * *
36842 TATATAACATATAG-TTTAAAAACATTTTTTAAAAT
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAA
* * **
36877 TTTATAATATAT-GATTTTAAAAAAATATTTTTGAAATG
1 TATATAATATATAG-TTTT--AAAAACATTTTTGAAAAA
*
36915 TATATTATATATAGTTTT-AAAACAATTTTT
1 TATATAATATATAGTTTTAAAAAC-ATTTTT
36945 TTTAGTATAT
Statistics
Matches: 202, Mismatches: 25, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
32 11 0.05
33 28 0.14
34 12 0.06
35 48 0.24
36 44 0.22
37 7 0.03
38 38 0.19
39 5 0.02
40 9 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAAACATTTTTGAAAAA
Found at i:36742 original size:106 final size:104
Alignment explanation
Indices: 36653--36944 Score: 252
Period size: 106 Copynumber: 2.7 Consensus size: 104
36643 GCAAATGGTG
* *
36653 TTTGAAAATACGTATATAATATAT-AGTTTT-CAAAACATTTTTGAAAAATATATATTATATAGT
1 TTTGAAAATA--TATATAATATATAAGTTTTAAAAAACATTTTT-AAAAACATATA--ATATAG-
* * *
36716 TTTTAAAACATTTTTAAAAATTATATATATAATTTTTAAAATAAT
60 TTTTAAAACATTTTTAAAAATCATATATATAAGTTTGAAAATAAT
*
36761 TTTGAAAATATATATAATATATAATTTTTGAAAAAACATTTTTAAAAACATATAATATAGTTTTA
1 TTTGAAAATATATATAATATATAAGTTTT-AAAAAACATTTTTAAAAACATATAATATAGTTTTA
* * * * *
36826 AAACATTTTTGAAAA-CTATATAACATATAGTTTAAAAACATT
65 AAACATTTTTAAAAATC-ATAT-ATATA-AGTTTGAAAATAAT
* * * * ***
36868 TTTTAAAAT-TTTATAATATATGA-TTTTAAAAAAATATTTTTGAAATGTATATTATATATAGTT
1 TTTGAAAATATATATAATATATAAGTTTT-AAAAAACATTTTT-AAAAACATA-TA-ATATAGTT
36931 TTAAAACAATTTTT
62 TTAAAAC-ATTTTT
36945 TTTAGTATAT
Statistics
Matches: 156, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
105 39 0.25
106 40 0.26
107 25 0.16
108 35 0.22
109 17 0.11
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (104 bp):
TTTGAAAATATATATAATATATAAGTTTTAAAAAACATTTTTAAAAACATATAATATAGTTTTAA
AACATTTTTAAAAATCATATATATAAGTTTGAAAATAAT
Found at i:36909 original size:73 final size:68
Alignment explanation
Indices: 36667--36944 Score: 249
Period size: 73 Copynumber: 3.9 Consensus size: 68
36657 AAAATACGTA
* *
36667 TATAATATAT-AGTTTTCAAAACATTTTTGAAAAATATATATTATATAGTTTTTAAAACATTTTT
1 TATAATATATGA-TTTT-AAAACATTTTTGAAAAATATATAATATATAG-TTTAAAAACATTTTT
36731 AAAAAT
63 AAAAAT
* * * *
36737 TAT-ATATATAATTTTTAAAATAATTTTGAAAATATATATAATATATAATTTTTGAAAAAACATT
1 TATAATATATGA-TTTTAAAACATTTTTGAAAA-ATATATAATATAT-A-GTTT--AAAAACATT
*
36801 TTTAAAAACA
60 TTTAAAAA-T
* *
36811 TATAATATA-G-TTTTAAAACATTTTTGAAAACTATATAACATATAGTTTAAAAACATTTTTTAA
1 TATAATATATGATTTTAAAACATTTTTGAAAAATATATAATATATAGTTTAAAAACA-TTTTTAA
*
36874 AATTT
65 AA-AT
* ** * *
36879 TATAATATATGATTTTAAAAAAATATTTTTGAAATGTATATTATATATAGTTTTAAAACAATTTT
1 TATAATATATGATTTT---AAAACATTTTTGAAAAATATATAATATATAGTTTAAAAAC-ATTTT
36944 T
62 T
36945 TTTAGTATAT
Statistics
Matches: 171, Mismatches: 21, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
67 7 0.04
68 18 0.11
69 24 0.14
70 25 0.15
71 15 0.09
72 18 0.11
73 55 0.32
74 4 0.02
75 5 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (68 bp):
TATAATATATGATTTTAAAACATTTTTGAAAAATATATAATATATAGTTTAAAAACATTTTTAAA
AAT
Found at i:36986 original size:17 final size:17
Alignment explanation
Indices: 36964--36996 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36954 TGTTATATAG
*
36964 TTTTTATTTATTATTTA
1 TTTTTATTCATTATTTA
36981 TTTTTATTCATTATTT
1 TTTTTATTCATTATTT
36997 TTATTCACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTCATTATTTA
Found at i:36988 original size:13 final size:13
Alignment explanation
Indices: 36978--37003 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36968 TATTTATTAT
36978 TTATTTTTATTCA
1 TTATTTTTATTCA
36991 TTATTTTTATTCA
1 TTATTTTTATTCA
37004 CCCGTTTTCA
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTTATTCA
Found at i:38119 original size:3 final size:3
Alignment explanation
Indices: 38111--38138 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38101 ATGGTAACTC
38111 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38139 GTTTCATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38210 original size:22 final size:21
Alignment explanation
Indices: 38182--38233 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
38172 ATATTTTTAT
* *
38182 TTTTATTTGTCTGTTTTATTTG
1 TTTTATTTGTC-CTTTGATTTG
*
38204 TTTTATTTTTCCTTTGATTTG
1 TTTTATTTGTCCTTTGATTTG
38225 TCTTTATTT
1 T-TTTATTT
38234 TTTTTATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTATTTGTCCTTTGATTTG
Found at i:40505 original size:2 final size:2
Alignment explanation
Indices: 40498--40530 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40488 TTTATGTATG
40498 TA TA TA TA 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 TA TA TA TA T
40531 TCATTTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42164 original size:27 final size:27
Alignment explanation
Indices: 42131--42190 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
42121 ATCGCCCTCT
*
42131 TGCTCCATGTCAAGACTGATGAGCCCC
1 TGCTCCATGTCAAGACAGATGAGCCCC
42158 TGCTCCATGTCAAGACAGATGAGCCCC
1 TGCTCCATGTCAAGACAGATGAGCCCC
42185 TGCTCC
1 TGCTCC
42191 GAGCATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.22
Consensus pattern (27 bp):
TGCTCCATGTCAAGACAGATGAGCCCC
Found at i:51287 original size:11 final size:11
Alignment explanation
Indices: 51271--51305 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
51261 CCCTAAATTG
51271 AAAAAAATAGA
1 AAAAAAATAGA
51282 AAAAAAATAG-
1 AAAAAAATAGA
51292 -AAAAAATAGA
1 AAAAAAATAGA
51302 AAAA
1 AAAA
51306 CAAACAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAAAATAGA
Found at i:51295 original size:8 final size:9
Alignment explanation
Indices: 51272--51305 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
51262 CCTAAATTGA
51272 AAAAAATAG
1 AAAAAATAG
51281 AAAAAAAATAG
1 --AAAAAATAG
51292 AAAAAATAG
1 AAAAAATAG
51301 AAAAA
1 AAAAA
51306 CAAACAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAAATAG
Found at i:52323 original size:94 final size:95
Alignment explanation
Indices: 52077--52894 Score: 1158
Period size: 94 Copynumber: 8.4 Consensus size: 95
52067 TACCCAGAGT
*
52077 CAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52142 GGACCGCTGGTTGTCAATAAACAATTTCAGAGC
66 GGACCGCTGGTTGTCAATAAACAATTTC--A-C
* *
52175 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52240 GGACCGCTGGTTGTCAATAAACAATTTC-C
66 GGACCGCTGGTTGTCAATAAACAATTTCAC
* * *
52269 TAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
52334 GGACCGCTGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
66 GGACCGCTGGTTGTCAATAAACAA--T-----T-TC--A-C
* * * *
52375 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCAAGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52440 GGACCGCTGGTTGTCAATAAACAATTTC-C
66 GGACCGCTGGTTGTCAATAAACAATTTCAC
52469 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
52534 GGACCCCTGGTTGTCAATAAACAATTTC-C
66 GGACCGCTGGTTGTCAATAAACAATTTCAC
* *
52563 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
52628 GGACCGCTGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
66 GGACCGCTGGTTGTCAATAAACAA--T-----T-TC--A-C
* *
52669 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52734 GGACCGCTGGTTGTCAATAAACAATTTC-C
66 GGACCGCTGGTTGTCAATAAACAATTTCAC
* * *
52763 CAATTTCAACTTCACAACGAAGGATAATGGACTCCAGACAACGTAAGTTCAACTTCACTACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
52828 GGACCGCTGGTTGTCAGTTAACAATTTCAGAGC
66 GGACCGCTGGTTGTCAATAAACAATTTC--A-C
52861 CAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAATTTCAACTTCACAACGAAGGATATTGGACTC
52895 GAAACAACAC
Statistics
Matches: 657, Mismatches: 35, Indels: 56
0.88 0.05 0.07
Matches are distributed among these distances:
94 346 0.53
96 2 0.00
98 128 0.19
99 2 0.00
101 2 0.00
102 4 0.01
104 2 0.00
106 171 0.26
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (95 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAACAATTTCAC
Found at i:52467 original size:200 final size:189
Alignment explanation
Indices: 52077--52894 Score: 1154
Period size: 200 Copynumber: 4.2 Consensus size: 189
52067 TACCCAGAGT
*
52077 CAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52142 GGACCGCTGGTTGTCAATAAACAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 GGACCGCTGGTTGTCAATAAACAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
52207 TCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTC-C
127 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCAC
* * *
52269 TAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
52334 GGACCGCTGGTTGTCAACAAACAATTTCCCAATCTCGGAGCCAATTTCAACTTCACAGCGAAGTA
66 GGACCGCTGGTTGTCAATAAACAA--T-----T-TC----CCAATTTCAACTTCACAACGAAGGA
* *
52399 TATTGGACTCCAGACAACGCAAGTTCAACTTCAAGATGAAGGGACCGCTGGTTGTCAATAAACAA
119 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
52464 TTTC-C
184 TTTCAC
52469 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
52534 GGACCCCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
66 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
* *
52599 GACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATCTC
131 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA--T-----T-TC
52664 GGAGC
188 --A-C
* *
52669 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
52734 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATAATGGACTCCA
66 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
* * * *
52799 GACAACGTAAGTTCAACTTCACTACGAAGGGACCGCTGGTTGTCAGTTAACAATTTCAGAGC
131 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC--A-C
52861 CAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAATTTCAACTTCACAACGAAGGATATTGGACTC
52895 GAAACAACAC
Statistics
Matches: 574, Mismatches: 32, Indels: 40
0.89 0.05 0.06
Matches are distributed among these distances:
188 85 0.15
190 1 0.00
192 124 0.22
193 2 0.00
194 1 0.00
195 1 0.00
196 2 0.00
198 2 0.00
199 1 0.00
200 355 0.62
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (189 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCAC
Found at i:52521 original size:43 final size:43
Alignment explanation
Indices: 52473--52628 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
52463 ATTTCCCAAT
52473 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
52516 TTCAACTTCACGACGAAGGGACCCCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
* *
52567 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
52610 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
52629 GACCGCTGGT
Statistics
Matches: 81, Mismatches: 24, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
43 36 0.44
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:52610 original size:294 final size:294
Alignment explanation
Indices: 52077--52894 Score: 1429
Period size: 294 Copynumber: 2.8 Consensus size: 294
52067 TACCCAGAGT
* * *
52077 CAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52142 GGACCGCTGGTTGTCAATAAACAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 GGACCGCTGGTTGTCAATAAACAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
52207 TCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCTAA
127 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAA
52272 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGA
192 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGA
52337 CCGCTGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
257 CCGCTGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
* *
52375 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCAAGATGAAG
1 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
52440 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
66 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
*
52505 GACAACGCAAGTTCAACTTCACGACGAAGGGACCCCTGGTTGTCAATAAACAATTTCCCAATTTC
131 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
52570 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGC
196 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGC
52635 TGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
261 TGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
52669 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
52734 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATAATGGACTCCA
66 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
* * * *
52799 GACAACGTAAGTTCAACTTCACTACGAAGGGACCGCTGGTTGTCAGTTAACAATTTCAGAGCCAA
131 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC----CCAA
*
52864 TTTCAACTTCACAACGAAGGATATTGGACTC
192 TTTCAACTTCACAGCGAAGGATATTGGACTC
52895 GAAACAACAC
Statistics
Matches: 498, Mismatches: 18, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
294 376 0.76
298 122 0.24
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (294 bp):
CAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
AACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACAATTTCCCAATCTCGGAGC
Found at i:54931 original size:2 final size:2
Alignment explanation
Indices: 54924--54960 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54914 TATGTATGTG
54924 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
54961 TCATTTTACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67326 original size:15 final size:15
Alignment explanation
Indices: 67306--67387 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
67296 TTCCGGAAAA
*
67306 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
67321 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
67336 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
67351 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
67366 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
67380 TGAATTAC
1 TGAATTAC
67388 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:67351 original size:45 final size:44
Alignment explanation
Indices: 67300--67387 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
67290 TTGGTTTTCC
* **
67300 GGAAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACT
67345 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
67388 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACT
Found at i:67385 original size:29 final size:30
Alignment explanation
Indices: 67306--67387 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
67296 TTCCGGAAAA
***
67306 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
67336 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
67366 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
67388 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:67393 original size:20 final size:20
Alignment explanation
Indices: 67370--67419 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
67360 GGAATTTGAA
67370 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
67390 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
67410 TTCTGGAAAA
1 TTCTGGAAAA
67420 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:67672 original size:30 final size:28
Alignment explanation
Indices: 67615--67710 Score: 99
Period size: 28 Copynumber: 3.3 Consensus size: 28
67605 CTTTACTAAA
*
67615 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAAAAATATTAT
67644 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAA--TATTAT
*
67674 ATATTATTAAA-ATAAAATAAAATATCT-T
1 ATATTATTAAATATATAA-AAAATAT-TAT
67702 ATATTATTA
1 ATATTATTA
67711 TAATGTAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
28 27 0.46
29 12 0.20
30 19 0.32
31 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:67765 original size:30 final size:30
Alignment explanation
Indices: 67619--67780 Score: 90
Period size: 31 Copynumber: 5.4 Consensus size: 30
67609 ACTAAAATAT
*
67619 TATTGAAATATATAA-ATAATATTATTCAT--
1 TATT-AAAAATATAATATAATATTATT-ATAA
* *
67648 TATTAAATATATAA-AAAAT-TTATTAT-A
1 TATTAAAAATATAATATAATATTATTATAA
* * * *
67675 TATTATTAAAATAAAATAAAATA-TCTTATAT
1 TATTA--AAAATATAATATAATATTATTATAA
* * * *
67706 TATT-ATAATGTAAT-TGATTATTTTATATAA
1 TATTAAAAATATAATAT-AATATTAT-TATAA
67736 TATTAAAAATATAATATAATATTATTATAAA
1 TATTAAAAATATAATATAATATTATTAT-AA
67767 TATTAATAAATATA
1 TATTAA-AAATATA
67781 TTTTAAATAT
Statistics
Matches: 104, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
26 2 0.02
27 10 0.10
28 24 0.23
29 13 0.12
30 21 0.20
31 26 0.25
32 8 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (30 bp):
TATTAAAAATATAATATAATATTATTATAA
Found at i:67775 original size:10 final size:10
Alignment explanation
Indices: 67734--67779 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
67724 TATTTTATAT
67734 AATATTAA-A
1 AATATTAATA
67743 AATA-TAATA
1 AATATTAATA
67752 TAATATTATTATA
1 -AATATTA--ATA
67765 AATATTAATA
1 AATATTAATA
67775 AATAT
1 AATAT
67780 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:67782 original size:21 final size:22
Alignment explanation
Indices: 67735--67791 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
67725 ATTTTATATA
*
67735 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATATAAT
67756 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
67778 ATATTTTAAATATT
1 ATATTATAAATATT
67792 TTAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:67796 original size:23 final size:21
Alignment explanation
Indices: 67742--67791 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
67732 ATAATATTAA
*
67742 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
67764 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
67785 AAATATT
1 AAATATT
67792 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:68039 original size:42 final size:42
Alignment explanation
Indices: 67980--68091 Score: 197
Period size: 42 Copynumber: 2.7 Consensus size: 42
67970 ATGAATTATA
* *
67980 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
68022 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
*
68064 TTCCGAAAAACGAATTACGTGAAACAAA
1 TTCCGGAAAACGAATTACGTGAAACAAA
68092 TACTGAAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
Found at i:77884 original size:20 final size:20
Alignment explanation
Indices: 77861--77901 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
77851 AATTGCGAAG
77861 CGAATATGTAAATCGCAACA
1 CGAATATGTAAATCGCAACA
* *
77881 CGAATTTGTAATTCGCAACA
1 CGAATATGTAAATCGCAACA
77901 C
1 C
77902 AGAAGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (20 bp):
CGAATATGTAAATCGCAACA
Found at i:78107 original size:22 final size:21
Alignment explanation
Indices: 78063--78107 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
78053 TCTCTCTCTA
* * *
78063 CGGCGACATCTGTCCCATCTC
1 CGGCGAAATCCGTCCCATATC
78084 CGGCGAAATCCGTCCCCATATC
1 CGGCGAAATCCGT-CCCATATC
78106 CG
1 CG
78108 ACGACCCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.18, C:0.42, G:0.20, T:0.20
Consensus pattern (21 bp):
CGGCGAAATCCGTCCCATATC
Found at i:80053 original size:42 final size:42
Alignment explanation
Indices: 79994--80092 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
79984 CCCCCCACTT
* * *
79994 CGAGAGCCATCACCTGATCGAGCCGATTCTATAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAGCTCCACAC
*
80036 CGAGAGCCATCACCTGATCGAGCCGATTATACATCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAGCTCCACAC
*
80078 TGAGAGCCATCACCT
1 CGAGAGCCATCACCT
80093 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACAGCTCCACAC
Found at i:80255 original size:21 final size:21
Alignment explanation
Indices: 80207--80256 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
80197 GTAAGGGGAG
80207 TTACGTGATGAGGTCAGTGAT
1 TTACGTGATGAGGTCAGTGAT
* *
80228 TTGCGTGATGAGGTCGGT-ACT
1 TTACGTGATGAGGTCAGTGA-T
80249 TTACGTGA
1 TTACGTGA
80257 CGACAATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTGAT
Found at i:80297 original size:21 final size:21
Alignment explanation
Indices: 80273--80369 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 21
80263 TGGTGCATGG
*
80273 CGTGATGAGGTACGGT-TTTTA
1 CGTGATGAGGTA-GATGTTTTA
*
80294 CGTGGTGAGGTAGATGTTTTA
1 CGTGATGAGGTAGATGTTTTA
* ** *
80315 CGCGATGACAATAG-TGCTTTA
1 CGTGATGA-GGTAGATGTTTTA
* ** **
80336 CGTGGTGAGGTATCTACTTTA
1 CGTGATGAGGTAGATGTTTTA
80357 CGTGATGAGGTAG
1 CGTGATGAGGTAG
80370 TTTTACGCGA
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
20 4 0.07
21 51 0.88
22 3 0.05
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.34
Consensus pattern (21 bp):
CGTGATGAGGTAGATGTTTTA
Found at i:80315 original size:63 final size:60
Alignment explanation
Indices: 80248--80429 Score: 188
Period size: 60 Copynumber: 3.0 Consensus size: 60
80238 AGGTCGGTAC
* * * *
80248 TTTACGTGACGACAATGGTGCATGGCGTGATGAGGTA-CGGT-TTTTACGTGGTGAGGTAGATGT
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATC--TACTTTACGTGATGAGGT--A-GT
* * * * *
80311 TTTACGCGATGACAATAGTGCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTAGT
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGT
* * * *
80371 TTTACGCGACGACAATGGTGCTTTACATGGTGAGGTATCTACTTTACGTGATGAGGTAG
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAG
80430 CCGCTCTACG
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
60 58 0.55
61 1 0.01
62 1 0.01
63 44 0.42
64 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (60 bp):
TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCTACTTTACGTGATGAGGTAGT
Found at i:80393 original size:60 final size:60
Alignment explanation
Indices: 80290--80429 Score: 217
Period size: 60 Copynumber: 2.3 Consensus size: 60
80280 AGGTACGGTT
* * *
80290 TTTACGTGGTGAGGTAGATGTTTTACGCGATGACAATAGTGCTTTACGTGGTGAGGTATCTAC
1 TTTACGTGATGAGGT--A-GTTTTACGCGACGACAATAGTGCTTTACATGGTGAGGTATCTAC
*
80353 TTTACGTGATGAGGTAGTTTTACGCGACGACAATGGTGCTTTACATGGTGAGGTATCTAC
1 TTTACGTGATGAGGTAGTTTTACGCGACGACAATAGTGCTTTACATGGTGAGGTATCTAC
80413 TTTACGTGATGAGGTAG
1 TTTACGTGATGAGGTAG
80430 CCGCTCTACG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
60 58 0.79
61 1 0.01
63 14 0.19
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (60 bp):
TTTACGTGATGAGGTAGTTTTACGCGACGACAATAGTGCTTTACATGGTGAGGTATCTAC
Found at i:80811 original size:20 final size:21
Alignment explanation
Indices: 80726--80814 Score: 65
Period size: 21 Copynumber: 4.3 Consensus size: 21
80716 TGTCATCGTC
*
80726 CAAGAGGCCCCTC-CTATCGTT
1 CAAGAGGCCCCTCAC-ACCGTT
*** * **
80747 CAAGAGGCTTATCCCACTATT
1 CAAGAGGCCCCTCACACCGTT
* **
80768 CAAGAGGCCCCTCTCATTGTT
1 CAAGAGGCCCCTCACACCGTT
80789 CAAGAGGCCCC-CACACCGTT
1 CAAGAGGCCCCTCACACCGTT
80809 CAAGAG
1 CAAGAG
80815 CCCGATTCAC
Statistics
Matches: 52, Mismatches: 15, Indels: 3
0.74 0.21 0.04
Matches are distributed among these distances:
20 12 0.23
21 39 0.75
22 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
CAAGAGGCCCCTCACACCGTT
Found at i:82320 original size:29 final size:29
Alignment explanation
Indices: 82287--82359 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
82277 TTTTCATTGC
* *
82287 GAATTTGTCTTTCGCAACAATCGTAACAT
1 GAATTTGACTTTCGCAACAATCGCAACAT
*
82316 GAATTTGACTTTCGCAACAATCGCAACGT
1 GAATTTGACTTTCGCAACAATCGCAACAT
*
82345 AAATTTGACTTTCGC
1 GAATTTGACTTTCGC
82360 GTGCGAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (29 bp):
GAATTTGACTTTCGCAACAATCGCAACAT
Done.