Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007523.1 Hibiscus syriacus cultivar Beakdansim tig00020977_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: 117890
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:5556 original size:21 final size:20
Alignment explanation
Indices: 5532--5580 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5522 CTCAAAATCA
* *
5532 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
5552 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
5572 -CTTTCAAAA
1 TTTTTCAAAA
5581 AAATCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:6077 original size:3 final size:3
Alignment explanation
Indices: 6065--6105 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
6055 TTCTTTTTTG
6065 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTCC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT
6106 TGGAGTTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:9750 original size:42 final size:42
Alignment explanation
Indices: 9671--9794 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 42
9661 TCACTAATGC
* * *
9671 CAATAGGTCATGTTTTATAGCGGCGTTTTTTATACAAACGCCG
1 CAATAAGTCATGTTCTATA-CGGCGTTTTTTACACAAACGCCG
*
9714 CAATAAGTCATGTTCTATACGGCGTTTTTTACACAAACGCTG
1 CAATAAGTCATGTTCTATACGGCGTTTTTTACACAAACGCCG
* * *
9756 CAACAAGTCAAG--CATATAACGGC-TTTTTTACATAAACGC
1 CAATAAGTCATGTTC-TAT-ACGGCGTTTTTTACACAAACGC
9795 TACAAGCCTG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 18 0.25
42 36 0.50
43 17 0.24
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (42 bp):
CAATAAGTCATGTTCTATACGGCGTTTTTTACACAAACGCCG
Found at i:10743 original size:18 final size:18
Alignment explanation
Indices: 10717--10751 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10707 ACACCAAATT
*
10717 TCAAGAATACTTTTAATC
1 TCAAGAATAATTTTAATC
*
10735 TCAATAATAATTTTAAT
1 TCAAGAATAATTTTAAT
10752 AGACACTACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (18 bp):
TCAAGAATAATTTTAATC
Found at i:14902 original size:227 final size:222
Alignment explanation
Indices: 14495--14905 Score: 606
Period size: 222 Copynumber: 1.8 Consensus size: 222
14485 CCAGTAGCAA
** * * * *
14495 TTATTTAATGTAATAGGTAGTACATGTTTAAAGTTGATGAGGTCTTAAAAATTCGAATAATAAAA
1 TTATTTAATGTAATAGGTAACACATGTTTAAAGCTGATGAGGCCTTAAAAATCCGAATAACAAAA
*
14560 TATGTTAATTACTTAATTTGTTATCAGTAATCAACATATTAGGTAGCGCCTAAAATGTTACCAAA
66 TAGGTTAATTACTTAATTTGTTATCAGTAATCAACATATTAGGTAGCGCCTAAAATGTTACCAAA
* *
14625 GTTTAAGTTGATGGAGCCTTAGAAAACCGACGATAACACAATAGGTTAATTACTAGAAACATTAT
131 GTTTAAGTTGATGGAACCTTAGAAAACCGACGATAACAAAATAGGTTAATTACTAGAAACATTAT
14690 CAACCATAATAACTTAACAAGTAGCGC
196 CAACCATAATAACTTAACAAGTAGCGC
* *
14717 TTATTTAATGTAATAGGTAACGCATGTTTAAAGCTGATGAGGCCTTAGAAATCCGACGATAACAA
1 TTATTTAATGTAATAGGTAACACATGTTTAAAGCTGATGAGGCCTTAAAAATCCGA--ATAACAA
* * * *
14782 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCTACATATTAGGTAGTGTCTAAAATGTTAC
64 AATAGGTTAATTACTTAATTTGTTATCAGTA--ATCAACATATTAGGTAGCGCCTAAAATGTTAC
* * **
14847 CAAAGTTTAAAGTTGATGGAATCTTAGAAATCCGGTGATAACAAAATAGGTTAATTACT
127 CAAAGTTT-AAGTTGATGGAACCTTAGAAAACCGACGATAACAAAATAGGTTAATTACT
14906 TGATTTGCTA
Statistics
Matches: 165, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
222 49 0.30
224 35 0.21
226 37 0.22
227 44 0.27
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (222 bp):
TTATTTAATGTAATAGGTAACACATGTTTAAAGCTGATGAGGCCTTAAAAATCCGAATAACAAAA
TAGGTTAATTACTTAATTTGTTATCAGTAATCAACATATTAGGTAGCGCCTAAAATGTTACCAAA
GTTTAAGTTGATGGAACCTTAGAAAACCGACGATAACAAAATAGGTTAATTACTAGAAACATTAT
CAACCATAATAACTTAACAAGTAGCGC
Found at i:15448 original size:200 final size:199
Alignment explanation
Indices: 15089--15633 Score: 677
Period size: 200 Copynumber: 2.7 Consensus size: 199
15079 GTTTAGATCG
* * * * * *
15089 AAAGTAACGATACTTATACAAAAAATATTGATACTTTATGTTTACGCCTATTATCATTAAACCGG
1 AAAGTATCGATACATATACAAAGAGTATTGATACTTTATGTTTACGCCTATTATCATTAAATCGA
* * *
15154 TAGATTTTTACCGTTTATATTATAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATA
66 TAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTATA
** **
15219 AGTATCGATACTTGTGATATGTGTATCGATACTTTCTGCGCACATGTTGTTTGAGAAGCATACTG
131 AGTATCGATACTTGTGATACATGTATCGATACTTTCTGCGCACAAATTG-TTGAGAAGCATACTG
*
15284 GACTA
195 GACCA
* *
15289 AAAGTATCGATATC-TATACAAAGAGTATCGATACTTTATGTTTACGCGTATTATCATTAAATCG
1 AAAGTATCGATA-CATATACAAAGAGTATTGATACTTTATGTTTACGCCTATTATCATTAAATCG
*
15353 ATAGATTTTTACCGTTTACATTATAAATTTACCTATAACTTTAAAGTAATTGGTTTCAAAATTAT
65 ATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTAT
* * * ** *
15418 AAGTATCGATACTTGTTATACATTTATCGATACTTTGTGCGTGCAAATTGTTGAGAAGCGTACTG
130 AAGTATCGATACTTGTGATACATGTATCGATACTTTCTGCGCACAAATTGTTGAGAAGCATACTG
15483 GACCA
195 GACCA
* * * *
15488 AAAATATCGATACATATACAAAGAGTATTGATACTTCATGTTTACGCCTATTATTAGGT--ATCG
1 AAAGTATCGATACATATACAAAGAGTATTGATACTTTATGTTTACGCCTATTATCA-TTAAATCG
* * * * *
15551 AGGTTCA-ATATATTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAACAT-GTTTCAA
65 A---T-AGAT-TTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGTAA-TTGGTTTCAA
*
15614 AATTATAAGAATCGATACTT
124 AATTATAAGTATCGATACTT
15634 ATATAACAGT
Statistics
Matches: 301, Mismatches: 35, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
198 6 0.02
199 67 0.22
200 158 0.52
201 4 0.01
202 65 0.22
203 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (199 bp):
AAAGTATCGATACATATACAAAGAGTATTGATACTTTATGTTTACGCCTATTATCATTAAATCGA
TAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGTAATTGGTTTCAAAATTATA
AGTATCGATACTTGTGATACATGTATCGATACTTTCTGCGCACAAATTGTTGAGAAGCATACTGG
ACCA
Found at i:15653 original size:20 final size:20
Alignment explanation
Indices: 15628--15678 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
15618 ATAAGAATCG
*
15628 ATACTTATATAACAGTATCA
1 ATACTTATACAACAGTATCA
* *
15648 ATACTTGTACGACAGTATCA
1 ATACTTATACAACAGTATCA
*
15668 ATACTTGTACA
1 ATACTTATACA
15679 TTTACGCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
ATACTTATACAACAGTATCA
Found at i:18046 original size:20 final size:20
Alignment explanation
Indices: 18021--18063 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
18011 ACCGATTTTT
18021 TCATATTGAAACTGGGTTTG
1 TCATATTGAAACTGGGTTTG
*
18041 TCATATTGAAACTGGTTTTG
1 TCATATTGAAACTGGGTTTG
18061 TCA
1 TCA
18064 AATTTCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (20 bp):
TCATATTGAAACTGGGTTTG
Found at i:18448 original size:20 final size:20
Alignment explanation
Indices: 18425--18479 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
18415 TATCTTTGCC
*
18425 GATTTTCTGAAATTTCAACT
1 GATTTTCTCAAATTTCAACT
* *
18445 GATTTTGTCAAATTTTAACT
1 GATTTTCTCAAATTTCAACT
* *
18465 GGTTTTGTC-AATTTC
1 GATTTTCTCAAATTTC
18480 CAATCGGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (20 bp):
GATTTTCTCAAATTTCAACT
Found at i:19043 original size:200 final size:199
Alignment explanation
Indices: 18536--19316 Score: 850
Period size: 200 Copynumber: 3.9 Consensus size: 199
18526 TATAGAGGCA
* * * * *
18536 GTATTGATACTTG-TATTTATGCCTATAATCAATATA-TCAGTAGACTTTTACCGTTTACATTGT
1 GTATTGATACTTGATGTTTACGCCTATTATCATTAAACT-AGTAGACTTTTACCGTTTACATTGT
* * * *
18599 AAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAATTCTGCATATCGATACTTTATACATGTG
65 AAAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATTC-GCGTATCGATACTTTATACATGTA
** * * *
18664 TATCGATACTTTGTGCGTGTAAATTG-TTGAGAAGCATATTGGACTAAAAGTATTGATACCTATA
129 TATCGATACTTTGTTTGTGCAAATTGTTTGAGATGCATATTGGACTAAAAGTATTGATACTTATA
18728 CAAAAT
194 CAAAAT
* * * *
18734 GTATTGATACTTGATGTTTACG-CTATTATCATTAAATTGGTAGACTTTCACTC-TTTATATTGT
1 GTATTGATACTTGATGTTTACGCCTATTATCATTAAACTAGTAGACTTTTAC-CGTTTACATTGT
* * *
18797 AAAGTTACCTATAACTTTAAAATAATTGGTTTCGAAATTCCGCGTATTGATACTTTGTACATGTA
65 AAAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATT-CGCGTATCGATACTTTATACATGTA
* *
18862 TATCGATATTTTGTTTAGTGCAAATTGTTTGAGATGCATATTGGACTAAAAATATTGATACTTAT
129 TATCGATACTTTGTTT-GTGCAAATTGTTTGAGATGCATATTGGACTAAAAGTATTGATACTTAT
18927 ACAAAAT
193 ACAAAAT
** **
18934 GTATCAATACTTGATGTTTACGCCTATTATCATTAAACTAGTAGACTTTTATTGTTTACATTGTA
1 GTATTGATACTTGATGTTTACGCCTATTATCATTAAACTAGTAGACTTTTACCGTTTACATTGTA
*
18999 AAGTTACCTATAACTTTAAAATAATTGGTTTCGAAATTCGCGTATCGATACTTTATACATGTATA
66 AAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATTCGCGTATCGATACTTTATACATGTATA
* * * ** * * *
19064 TCGATACTTT-TTTGCATACATATTATTTGAGATATATACTGGAATAAAAGTATCGATACTATAT
131 TCGATACTTTGTTTG--TGCAAATTGTTTGAGATGCATATTGGACTAAAAGTATTGATACT-TAT
*
19128 A-ATAAT
193 ACAAAAT
* * * * * *
19134 -TATTGATACTTTATATTTACGCCTTTTATCATTAAACTGGTAGATTTTTACCGTTTTCATTGTA
1 GTATTGATACTTGATGTTTACGCCTATTATCATTAAACTAGTAGACTTTTACCGTTTACATTGTA
* * * *** *
19198 AATTTACCTATTACTTTAAAGA-AATAGGTTTCAAAATTATAAGTATC-AGTACATGTTATGCAT
66 AAGTTACCTATAACTTTAAA-ATAATAGGTTTCGAAATT-CGCGTATCGA-TAC-T-TTATACAT
* * * *
19261 G--TACCGATACTTT-TTGCGTACAAATTGTTTGAGATGCATATTGGAATAATAAGTAT
126 GTATATCGATACTTTGTT-TGTGCAAATTGTTTGAGATGCATATTGGACTAA-AAGTAT
19317 CAATACGTTA
Statistics
Matches: 497, Mismatches: 68, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
198 114 0.23
199 134 0.27
200 162 0.33
201 79 0.16
202 8 0.02
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (199 bp):
GTATTGATACTTGATGTTTACGCCTATTATCATTAAACTAGTAGACTTTTACCGTTTACATTGTA
AAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATTCGCGTATCGATACTTTATACATGTATA
TCGATACTTTGTTTGTGCAAATTGTTTGAGATGCATATTGGACTAAAAGTATTGATACTTATACA
AAAT
Found at i:19287 original size:399 final size:398
Alignment explanation
Indices: 18574--19305 Score: 926
Period size: 399 Copynumber: 1.8 Consensus size: 398
18564 TCAATATATC
* *
18574 AGTAGACTTTTACCGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTTTCGAAATTC
1 AGTAGACTTTTACCGTTTACATTGTAAAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATTC
* * ** *
18639 TGCATATCGATACTTTATACATGTGTATCGATACTTTGTGCGTGTAAATTGTTGAGAAGCATATT
66 TGCATATCGATACTTTATACATGTATATCGATACTTTGTGCATACAAATTGTTGAGAAGCATACT
* * *
18704 GGACTAAAAGTATTGATACCTATACAAAATGTATTGATACTTGATGTTTACGCTATTATCATTAA
131 GGAATAAAAGTATCGATACCTATACAAAATGTATTGATACTTGATATTTACGCTATTATCATTAA
* * *
18769 ATTGGTAGACTTTCACTCTTTATATTGTAAAGTTACCTATAACTTTAAAATAATTGGTTTCGAAA
196 ACTGGTAGACTTTCACTCTTTATATTGTAAAGTTACCTATAACTTTAAAATAATAGGTTTCAAAA
* ** * * * * * *
18834 TTCCGCGTATTGATACTTTGTACATGTATATCGATATTTTGTTTAGTGCAAATTGTTTGAGATGC
261 TTACAAGTATAGATACTTTATACATG-ATACCGATACTTTGTTGAGTACAAATTGTTTGAGATGC
18899 ATATTGGACTAAAAATATTGATACTTATACAAAATGTATCAATACTTGATGTTTACGCCTATTAT
325 ATATTGGACTAAAAATATTGATACTTATACAAAATGTATCAATACTTGATGTTTACGCCTATTAT
18964 CATTAAACT
390 CATTAAACT
** *
18973 AGTAGACTTTTATTGTTTACATTGTAAAGTTACCTATAACTTTAAAATAATTGGTTTCGAAATTC
1 AGTAGACTTTTACCGTTTACATTGTAAAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATTC
* * * * *
19038 -GCGTATCGATACTTTATACATGTATATCGATACTTTTTTGCATACATATTATTTGAGATA-TAT
66 TGCATATCGATACTTTATACATGTATATCGATAC-TTTGTGCATACAAATT-GTTGAGA-AGCAT
* * *
19101 ACTGGAATAAAAGTATCGATA-CTATATAATAAT-TATTGATACTTTATATTTACGCCTTTTATC
128 ACTGGAATAAAAGTATCGATACCTATACAA-AATGTATTGATACTTGATATTTACG-CTATTATC
* * * *
19164 ATTAAACTGGTAGATTTTTAC-CGTTT-TCATTGTAAATTTACCTATTACTTTAAAGA-AATAGG
191 ATTAAACTGGTAGACTTTCACTC-TTTAT-ATTGTAAAGTTACCTATAACTTTAAA-ATAATAGG
* * *
19226 TTTCAAAATTATAAGTATCAG-TACATGTTATGCATG-TACCGATACTTT-TTGCGTACAAATTG
253 TTTCAAAATTACAAGTAT-AGATAC-T-TTATACATGATACCGATACTTTGTTGAGTACAAATTG
19288 TTTGAGATGCATATTGGA
315 TTTGAGATGCATATTGGA
19306 ATAATAAGTA
Statistics
Matches: 282, Mismatches: 40, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
398 31 0.11
399 128 0.45
400 112 0.40
401 4 0.01
402 7 0.02
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (398 bp):
AGTAGACTTTTACCGTTTACATTGTAAAGTTACCTATAACTTTAAAATAATAGGTTTCGAAATTC
TGCATATCGATACTTTATACATGTATATCGATACTTTGTGCATACAAATTGTTGAGAAGCATACT
GGAATAAAAGTATCGATACCTATACAAAATGTATTGATACTTGATATTTACGCTATTATCATTAA
ACTGGTAGACTTTCACTCTTTATATTGTAAAGTTACCTATAACTTTAAAATAATAGGTTTCAAAA
TTACAAGTATAGATACTTTATACATGATACCGATACTTTGTTGAGTACAAATTGTTTGAGATGCA
TATTGGACTAAAAATATTGATACTTATACAAAATGTATCAATACTTGATGTTTACGCCTATTATC
ATTAAACT
Found at i:21347 original size:15 final size:15
Alignment explanation
Indices: 21327--21356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21317 TAAACCAAAC
21327 ATACAAAACAATGTT
1 ATACAAAACAATGTT
*
21342 ATACAAAACAGTGTT
1 ATACAAAACAATGTT
21357 CTAATAGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
ATACAAAACAATGTT
Found at i:22683 original size:15 final size:15
Alignment explanation
Indices: 22659--22688 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22649 CTTCAGCCTT
*
22659 AGCGTTTTCCATCGG
1 AGCGTCTTCCATCGG
22674 AGCGTCTTCCATCGG
1 AGCGTCTTCCATCGG
22689 TTGGTGTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.30, G:0.27, T:0.30
Consensus pattern (15 bp):
AGCGTCTTCCATCGG
Found at i:25909 original size:18 final size:19
Alignment explanation
Indices: 25888--25925 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
25878 ATATCTAAAC
*
25888 TTAACTTCATATTT-ATCT
1 TTAACTCCATATTTAATCT
*
25906 TTAACTCCTTATTTAATCT
1 TTAACTCCATATTTAATCT
25925 T
1 T
25926 CCAGTACCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAACTCCATATTTAATCT
Found at i:29757 original size:18 final size:18
Alignment explanation
Indices: 29736--29799 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
29726 AATCCCTTAC
*
29736 TTGAGAATAAGACCTTGG
1 TTGAGAAGAAGACCTTGG
*
29754 TTGAGAAGATGACCTTGG
1 TTGAGAAGAAGACCTTGG
***
29772 TTGAGAAGAAGGTTTTGG
1 TTGAGAAGAAGACCTTGG
29790 TTGAGAAGAA
1 TTGAGAAGAA
29800 CTGCATCTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.28
Consensus pattern (18 bp):
TTGAGAAGAAGACCTTGG
Found at i:30827 original size:200 final size:197
Alignment explanation
Indices: 30295--31524 Score: 1278
Period size: 200 Copynumber: 6.1 Consensus size: 197
30285 GTTTAGATCG
*
30295 AAAGTATCGATACCTATACAAAAAGTATCGATATTTTATGTTTACGCCTATTATCATTAAA-CTG
1 AAAGTATCGATA-CTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATC-G
** * * *
30359 GTAGATTTTTATTGTTTACATTGTAAATTTACCTAT-TA-CT-AAGTAATAGGTTTCGAAATTAT
64 GTAGA-TTTTACCGTTTACATTGTAAATTTACCTATAAATTTAAAGTAATCGGTTTCGAAATTAT
* * * ** * *
30421 AAGTATTGATA-TTTTTGATACGTGTATCGATACTTTCTGCGTGCATGTTTTTTTGAGAAACATA
128 AAGTATCGATACTTGTT-ATACATGTATCGATACTTTCTGCGTGCA--AATTGTTGAGAAGCATA
30485 CTGGACTA
190 CTGGACTA
* *
30493 AAAGTATTGATACCTATACAAAGAGTAAT-GATACTTTATGTTTACGCCTATTATCATTAAATCG
1 AAAGTATCGATA-CTATACAAAAAGT-ATCGATACTTTATGTTTACGCCTATTATCATTAAATCG
* ** *
30557 GTAGA-TTTACCGTTTACATTGTAAATTTACCAATAAATTTAAAGTAATCAATTTTGAAATTATA
64 GTAGATTTTACCGTTTACATTGTAAATTTACCTATAAATTTAAAGTAATCGGTTTCGAAATTATA
* * * * *
30621 AGTATCGATACTTGTTATACATGTATTGATACCTTGTGCGTGCAAATTGTTGAGAAGTTATATTG
129 AGTATCGATACTTGTTATACATGTATCGATACTTTCTGCGTGCAAATTGTTGAGAAG-CATACTG
30686 GACTA
193 GACTA
* *
30691 AAAGTATCGATATCTATACAAAAAGTATCGATACTCTATGTTTATGCCTATTATCATTAAATCGG
1 AAAGTATCGATA-CTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATCGG
* * *
30756 TAGACTTTTACCGTTGACATTGTAAATTTACCTATAAATTTAAAGTAATTGATTTCGAAATTATA
65 TAGA-TTTTACCGTTTACATTGTAAATTTACCTATAAATTTAAAGTAATCGGTTTCGAAATTATA
* * *
30821 AGTATCGATACTTGTTATACATGTATTGATACTTTGTGCGGGCAAATTGTTGAGAAGCATACTGG
129 AGTATCGATACTTGTTATACATGTATCGATACTTTCTGCGTGCAAATTGTTGAGAAGCATACTGG
30886 ACTA
194 ACTA
* * * * ** *
30890 AAAGTATTGATACATATACAAAGAGTATCAATATTTTATGTTTACATCTATTATCATTAAACCGG
1 AAAGTATCGATAC-TATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATCGG
* * * * * *
30955 TAGATTTTCATCGTTTTCATTGTAAAATTACCTATTACTTTAAAGTAATCGGTTTCAAAATTATA
65 TAGATTTT-ACCGTTTACATTGTAAATTTACCTATAAATTTAAAGTAATCGGTTTCGAAATTATA
* * * * * * * ** *
31020 GGTATTGATACTTGTGATACGTGTATAGATTCTTTCTGTGTGCATGTTGTTTGAGAAGCATATTG
129 AGTATCGATACTTGTTATACATGTATCGATACTTTCTGCGTGCAAATTG-TTGAGAAGCATACTG
31085 GACTA
193 GACTA
* * * *
31090 AAAGTATCGATACATGTATAAAAAGTATCGATACTTTATGTTTACGTCTATTATCATTAAACCGG
1 AAAGTATCGATAC-TATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATCGG
* * * * *
31155 TAGACTTTTACCGTTAACATTGTAAATTTACCTATAATTTTAAACTAACCGGTTTTGAAATTATA
65 TAGA-TTTTACCGTTTACATTGTAAATTTACCTATAAATTTAAAGTAATCGGTTTCGAAATTATA
* * * *
31220 AGTATCGATA-TTGGTTATACATGTATCGATACTTTATGCGGGCAAATTGTTAAGAAGCATACTA
129 AGTATCGATACTT-GTTATACATGTATCGATACTTTCTGCGTGCAAATTGTTGAGAAGCATACTG
31284 GACTA
193 GACTA
* * * *
31289 AAAGTATTGATATCTATAC---GAGTATCGATACTTTATGTTTATGCCTATTATCATTAAATTGG
1 AAAGTATCGATA-CTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATCGG
* * * *
31351 TAGATTTTTACCGTTTTCATTGTAAAATTA-TTATATATATTTCTTTAAAGTAATATGTATATGT
65 TAGA-TTTTACCGTTTACATTGTAAATTTACCTATA-A-A----TTTAAAGTAAT-CG-----GT
* * * * * * *
31415 TTTGAAATTATAAGTATCAATACTTGTTATACGTGTATCGATACTTTTTACGTACAAATTGTTTC
117 TTCGAAATTATAAGTATCGATACTTGTTATACATGTATCGATACTTTCTGCGTGCAAATTG-TTG
* * * *
31480 AGATGCACACTAGAATA
181 AGAAGCATACTGGACTA
* *
31497 AAAGTAGCGATACTTATATAAAAAGTAT
1 AAAGTATCGATAC-TATACAAAAAGTAT
31525 TGAAATTGGA
Statistics
Matches: 868, Mismatches: 130, Indels: 55
0.82 0.12 0.05
Matches are distributed among these distances:
195 4 0.00
196 91 0.10
197 12 0.01
198 138 0.16
199 241 0.28
200 276 0.32
201 13 0.01
202 1 0.00
207 55 0.06
208 32 0.04
211 5 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (197 bp):
AAAGTATCGATACTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATCGGT
AGATTTTACCGTTTACATTGTAAATTTACCTATAAATTTAAAGTAATCGGTTTCGAAATTATAAG
TATCGATACTTGTTATACATGTATCGATACTTTCTGCGTGCAAATTGTTGAGAAGCATACTGGAC
TA
Found at i:31087 original size:399 final size:394
Alignment explanation
Indices: 30295--31380 Score: 1389
Period size: 399 Copynumber: 2.7 Consensus size: 394
30285 GTTTAGATCG
*
30295 AAAGTATCGATACCTATACAAAAAGTATCGATATTTTATGTTTACGCCTATTATCATTAAACTGG
1 AAAGTATCGATA-CTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAAC-GG
* ** * * *
30360 TAGATTTTTATTGTTTACATTGTAAATTTACCTAT-TA-CT-AAGTAATAGGTTTCGAAATTATA
64 TAGACTTTTACCGTTAACATTGTAAATTTACCTATAAATTTAAAGTAATAGGTTTCGAAATTATA
* * * * * ** * *
30422 AGTATTGATATTTTTGATACGTGTATCGATACTTTCTGCGTGCATGTTTTTTTGAGAAACATACT
129 AGTATCGATATTGTT-ATACATGTATCGATACTTTATGCGGGCA--AATTGTTGAGAAGCATACT
30487 GGACTAAAAGTATTGATACCTATACAAAGAGTAAT-GATACTTTATGTTTACGCCTATTATCATT
191 GGACTAAAAGTATTGATA-CTATACAAAGAGT-ATCGATACTTTATGTTTACGCCTATTATCATT
* * **
30551 AAATCGGTAGA-TTTACCGTTTACATTGTAAATTTACCAATAAATTTAAAGTAATCAATTTTGAA
254 AAATCGGTAGATTTTACCGTTTTCATTGTAAAATTACCAATAAATTTAAAGTAATCAATTTCAAA
* * * *
30615 ATTATAAGTATCGATACTTGTTATACATGTATTGATACCTTGTGCGTGCAAATTGTTGAGAAGTT
319 ATTATAAGTATCGATACTTGTGATACATGTATAGATACCTTCTGCGTGCAAATTGTTGAGAAGTC
30680 ATATTGGACTA
384 ATATTGGACTA
* *
30691 AAAGTATCGATATCTATACAAAAAGTATCGATACTCTATGTTTATGCCTATTATCATTAAATCGG
1 AAAGTATCGATA-CTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAA-CGG
* * *
30756 TAGACTTTTACCGTTGACATTGTAAATTTACCTATAAATTTAAAGTAATTGATTTCGAAATTATA
64 TAGACTTTTACCGTTAACATTGTAAATTTACCTATAAATTTAAAGTAATAGGTTTCGAAATTATA
* *
30821 AGTATCGATACTTGTTATACATGTATTGATACTTTGTGCGGGCAAATTGTTGAGAAGCATACTGG
129 AGTATCGATA-TTGTTATACATGTATCGATACTTTATGCGGGCAAATTGTTGAGAAGCATACTGG
* * **
30886 ACTAAAAGTATTGATACATATACAAAGAGTATCAATATTTTATGTTTACATCTATTATCATTAAA
193 ACTAAAAGTATTGATAC-TATACAAAGAGTATCGATACTTTATGTTTACGCCTATTATCATTAAA
* * * * * **
30951 CCGGTAGATTTTCATCGTTTTCATTGTAAAATTACCTATTACTTTAAAGTAATCGGTTTCAAAAT
257 TCGGTAGATTTT-ACCGTTTTCATTGTAAAATTACCAATAAATTTAAAGTAATCAATTTCAAAAT
* * * * * * **
31016 TATAGGTATTGATACTTGTGATACGTGTATAGATTCTTTCTGTGTGCATGTTGTTTGAGAAG-CA
321 TATAAGTATCGATACTTGTGATACATGTATAGATACCTTCTGCGTGCAAATTG-TTGAGAAGTCA
31080 TATTGGACTA
385 TATTGGACTA
* * *
31090 AAAGTATCGATACATGTATAAAAAGTATCGATACTTTATGTTTACGTCTATTATCATTAAACCGG
1 AAAGTATCGATAC-TATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAA-CGG
* * ** *
31155 TAGACTTTTACCGTTAACATTGTAAATTTACCTATAATTTTAAACTAACCGGTTTTGAAATTATA
64 TAGACTTTTACCGTTAACATTGTAAATTTACCTATAAATTTAAAGTAATAGGTTTCGAAATTATA
* *
31220 AGTATCGATATTGGTTATACATGTATCGATACTTTATGCGGGCAAATTGTTAAGAAGCATACTAG
129 AGTATCGATATT-GTTATACATGTATCGATACTTTATGCGGGCAAATTGTTGAGAAGCATACTGG
*
31285 ACTAAAAGTATTGATATCTATAC---GAGTATCGATACTTTATGTTTATGCCTATTATCATTAAA
193 ACTAAAAGTATTGATA-CTATACAAAGAGTATCGATACTTTATGTTTACGCCTATTATCATTAAA
*
31347 TTGGTAGATTTTTACCGTTTTCATTGTAAAATTA
257 TCGGTAGA-TTTTACCGTTTTCATTGTAAAATTA
31381 TTATATATAT
Statistics
Matches: 602, Mismatches: 74, Indels: 28
0.86 0.11 0.04
Matches are distributed among these distances:
396 153 0.25
397 86 0.14
398 7 0.01
399 343 0.57
400 13 0.02
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (394 bp):
AAAGTATCGATACTATACAAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACGGTA
GACTTTTACCGTTAACATTGTAAATTTACCTATAAATTTAAAGTAATAGGTTTCGAAATTATAAG
TATCGATATTGTTATACATGTATCGATACTTTATGCGGGCAAATTGTTGAGAAGCATACTGGACT
AAAAGTATTGATACTATACAAAGAGTATCGATACTTTATGTTTACGCCTATTATCATTAAATCGG
TAGATTTTACCGTTTTCATTGTAAAATTACCAATAAATTTAAAGTAATCAATTTCAAAATTATAA
GTATCGATACTTGTGATACATGTATAGATACCTTCTGCGTGCAAATTGTTGAGAAGTCATATTGG
ACTA
Found at i:31453 original size:21 final size:19
Alignment explanation
Indices: 31428--31467 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
31418 GAAATTATAA
31428 GTATCAATACTTGTTATACGT
1 GTATCAATACTT-TT-TACGT
*
31449 GTATCGATACTTTTTACGT
1 GTATCAATACTTTTTACGT
31468 ACAAATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (19 bp):
GTATCAATACTTTTTACGT
Found at i:37168 original size:414 final size:412
Alignment explanation
Indices: 36450--37237 Score: 1074
Period size: 414 Copynumber: 1.9 Consensus size: 412
36440 ATTTTAATTA
* * *
36450 TAGTGACAAAATATACTGTCACGAAAATTTCCCTCTATATTTTTTTGCGACAAAAAAGTCATATT
1 TAGTAACAAAATATACTGTCACGAAAATTTCCCTCCATATTTTTTTGC-ACAAAAAAGTCATATA
*
36515 GTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAATGTTCACAAAAATAATACTA
65 GTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAATGTTCACAAAAATAATACTA
** * *
36580 TTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAATTTTAACTATAATGATAGCATATATTG
130 TTCACACTTTTGTGACAAATTATATTTGTAGCTATAAATTTTAACTATAATGATAACATATATTG
* *
36645 TCATAACTATTTTTTCTCAACTTTTTTATTTCAAAAGTTATATTGACAATTTTTATAATTATAAT
195 TCATAAATATTTTTTCTCAACTTTTTTATTTCAAAAGTTATATTGACAAGTTTTATAATTATAAT
* * *
36710 TTATAGTTATTGTTACAGAAAAAATTATTACATCAAATAATAAAATTCAAGTTTTTTGTAATAAA
260 TTATAGTTATTGTTACAGAAAAAATTATCACATCAAATAATAAAAATCAAGTTTTTGGTAATAAA
36775 TTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCAGAACCATTTCTCCCTA
325 TTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCAGAACCATTTCTCCCTA
36840 TCTTTAGTGTCAAAAATGCTATG
390 TCTTTAGTGTCAAAAATGCTATG
* * ** *
36863 TAGTAACAAAATATATTGTCA-TAAAGATTTTTCTCCATATTTTTTGTGC-CAAAAAA-TCTTAT
1 TAGTAACAAAATATACTGTCACGAAA-ATTTCCCTCCATATTTTTT-TGCACAAAAAAGTCATAT
36925 AGTAAC-AATTTTCGTAACTATAAGTG-T-ATAATTATTACAAAAAAAAACAT-TGTCACGAAAA
64 AGTAACAAATTTT-GTAACTATAAGTGTTAATAATTATTAC----AAAAA-ATGT-TCAC-AAAA
** * * *
36986 ATAATGGTATTCACACTTTTGTGGCAAATTATACTTT-TAGCTATAAATTTTAATTATAGTGATA
121 ATAATACTATTCACACTTTTGTGACAAATTATA-TTTGTAGCTATAAATTTTAACTATAATGATA
* * * * *
37050 ACATATATTGTGATAAATATTTTTT-TCCAC-TTTTTGTTTCAAAAATTTATATTGATAAGTTTT
185 ACATATATTGTCATAAATATTTTTTCTCAACTTTTTTATTTC-AAAAGTTATATTGACAAGTTTT
* * * *
37113 GTAATTATAATTTATAGTTATTGTTATAGAAAAAATTATCACATTAGATAATAAAAATCAAGTTT
249 ATAATTATAATTTATAGTTATTGTTACAGAAAAAATTATCACATCAAATAATAAAAATCAAGTTT
* * *
37178 TTGGTAATCAATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAATTATACTATCA
314 TTGGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCA
37238 ACAAAAATAA
Statistics
Matches: 328, Mismatches: 35, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
409 11 0.03
410 7 0.02
411 22 0.07
412 10 0.03
413 50 0.15
414 147 0.45
415 78 0.24
416 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (412 bp):
TAGTAACAAAATATACTGTCACGAAAATTTCCCTCCATATTTTTTTGCACAAAAAAGTCATATAG
TAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAATGTTCACAAAAATAATACTAT
TCACACTTTTGTGACAAATTATATTTGTAGCTATAAATTTTAACTATAATGATAACATATATTGT
CATAAATATTTTTTCTCAACTTTTTTATTTCAAAAGTTATATTGACAAGTTTTATAATTATAATT
TATAGTTATTGTTACAGAAAAAATTATCACATCAAATAATAAAAATCAAGTTTTTGGTAATAAAT
TATTTTTGTACTTATATATTTTAATCATTATGAAAAATAATACTATCAGAACCATTTCTCCCTAT
CTTTAGTGTCAAAAATGCTATG
Found at i:39355 original size:20 final size:21
Alignment explanation
Indices: 39330--39425 Score: 160
Period size: 20 Copynumber: 4.7 Consensus size: 21
39320 TTGCAGCCTT
*
39330 GATGCATGGATGCATGGCAA-
1 GATGCATCGATGCATGGCAAG
39350 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
39371 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
39391 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
39412 GATGCATCGATGCA
1 GATGCATCGATGCA
39426 CTAAATGCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
20 38 0.54
21 33 0.46
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:39387 original size:41 final size:41
Alignment explanation
Indices: 39330--39425 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
39320 TTGCAGCCTT
39330 GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
1 GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
*
39371 GATGCATGGATGCATGGCAGGATGCATCGATGCATGGCAAG
1 GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
*
39412 GATGCATCGATGCA
1 GATGCATGGATGCA
39426 CTAAATGCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (41 bp):
GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
Found at i:39514 original size:21 final size:21
Alignment explanation
Indices: 39488--39545 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
39478 CATTAGTGCA
39488 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
39509 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
*
39530 GATGCATAGATGCACT
1 GATGCATGGATGCACT
39546 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:39646 original size:29 final size:29
Alignment explanation
Indices: 39625--39682 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
39615 AAACTTTGAA
39625 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
39654 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
39683 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:39672 original size:30 final size:30
Alignment explanation
Indices: 39625--39684 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
39615 AAACTTTGAA
39625 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
39654 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
39685 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:41003 original size:19 final size:20
Alignment explanation
Indices: 40960--41007 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
40950 TCTAAATCCT
*
40960 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
40980 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
40999 TTTTCAAAA
1 TTTTCAAAA
41008 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:42326 original size:20 final size:21
Alignment explanation
Indices: 42301--42396 Score: 151
Period size: 20 Copynumber: 4.7 Consensus size: 21
42291 TTGCAGTCTT
*
42301 GATGCATGGATGCATGGCAA-
1 GATGCATCGATGCATGGCAAG
*
42321 GATGCATCGATGCATGGTAAG
1 GATGCATCGATGCATGGCAAG
*
42342 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
42362 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
42383 GATGCATCGATGCA
1 GATGCATCGATGCA
42397 CTAAATGCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
20 37 0.54
21 32 0.46
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:42358 original size:41 final size:41
Alignment explanation
Indices: 42301--42396 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
42291 TTGCAGTCTT
*
42301 GATGCATGGATGCATGGCAAGATGCATCGATGCATGGTAAG
1 GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
*
42342 GATGCATGGATGCATGGCAGGATGCATCGATGCATGGCAAG
1 GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
*
42383 GATGCATCGATGCA
1 GATGCATGGATGCA
42397 CTAAATGCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (41 bp):
GATGCATGGATGCATGGCAAGATGCATCGATGCATGGCAAG
Found at i:42485 original size:21 final size:21
Alignment explanation
Indices: 42459--42516 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
42449 CATTAGTGCA
42459 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
42480 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
*
42501 GATGCATAGATGCACT
1 GATGCATGGATGCACT
42517 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:42617 original size:29 final size:29
Alignment explanation
Indices: 42596--42653 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
42586 AAACTTTGAA
42596 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
42625 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
42654 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:42643 original size:30 final size:30
Alignment explanation
Indices: 42596--42655 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
42586 AAACTTTGAA
42596 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
42625 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
42656 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:47746 original size:40 final size:40
Alignment explanation
Indices: 47702--47778 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
47692 ATAGCTCTTT
*
47702 ACCGGATTTCTCAAATTGAAATCAATTTTGTCAAATTTCA
1 ACCGGATTTCTCAAATTCAAATCAATTTTGTCAAATTTCA
* * * * **
47742 ACCGGTTTTGTCAATTTCCAATCGGTTTTGTCAAATT
1 ACCGGATTTCTCAAATTCAAATCAATTTTGTCAAATT
47779 CGTTACATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (40 bp):
ACCGGATTTCTCAAATTCAAATCAATTTTGTCAAATTTCA
Found at i:47750 original size:20 final size:21
Alignment explanation
Indices: 47727--47778 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
47717 TTGAAATCAA
47727 TTTTGTCAAATTT-CAACCGG
1 TTTTGTCAAATTTCCAACCGG
*
47747 TTTTGTC-AATTTCCAATCGG
1 TTTTGTCAAATTTCCAACCGG
47767 TTTTGTCAAATT
1 TTTTGTCAAATT
47779 CGTTACATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.17
20 20 0.69
21 4 0.14
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.46
Consensus pattern (21 bp):
TTTTGTCAAATTTCCAACCGG
Found at i:49171 original size:25 final size:26
Alignment explanation
Indices: 49120--49176 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
49110 ATATATATAT
*
49120 ATATATATAAAAGTTTGTTTTTCAAC
1 ATATATATAAAAGTTTGTATTTCAAC
* * *
49146 ATATTTATCAAAG-TTGTATTTGAAC
1 ATATATATAAAAGTTTGTATTTCAAC
49171 AT-TATA
1 ATATATA
49177 CGAATATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.12
25 12 0.46
26 11 0.42
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (26 bp):
ATATATATAAAAGTTTGTATTTCAAC
Found at i:51687 original size:2 final size:2
Alignment explanation
Indices: 51680--51716 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51670 ATTAGAAGAA
51680 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
51717 TCCGTATACG
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53673 original size:16 final size:16
Alignment explanation
Indices: 53652--53710 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
53642 CGATGTTTAT
53652 TGCTCGTTAAGCTCGA
1 TGCTCGTTAAGCTCGA
** *
53668 TGCTCGTTGTTTGCCTCGT
1 TGCTCG-T-TAAG-CTCGA
53687 TGCTCGTTAAGCTCGA
1 TGCTCGTTAAGCTCGA
53703 TGCTCGTT
1 TGCTCGTT
53711 GCTTGTTTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 18 0.53
17 3 0.09
18 3 0.09
19 10 0.29
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.39
Consensus pattern (16 bp):
TGCTCGTTAAGCTCGA
Found at i:53692 original size:7 final size:7
Alignment explanation
Indices: 53651--53729 Score: 51
Period size: 7 Copynumber: 11.3 Consensus size: 7
53641 TCGATGTTTA
53651 TTGCTCG
1 TTGCTCG
53658 TTAAGCTCG
1 TT--GCTCG
*
53667 ATGCTCG
1 TTGCTCG
53674 TTG-T--
1 TTGCTCG
53678 TTGCCTCG
1 TTG-CTCG
53686 TTGCTCG
1 TTGCTCG
53693 TTAAGCTCG
1 TT--GCTCG
*
53702 ATGCTCG
1 TTGCTCG
*
53709 TTGCTTG
1 TTGCTCG
53716 TT--TCG
1 TTGCTCG
53721 TTGCTCG
1 TTGCTCG
53728 TT
1 TT
53730 AAGCTCATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
4 3 0.05
5 4 0.07
6 2 0.04
7 32 0.57
8 3 0.05
9 12 0.21
ACGTcount: A:0.08, C:0.24, G:0.25, T:0.43
Consensus pattern (7 bp):
TTGCTCG
Found at i:53697 original size:35 final size:35
Alignment explanation
Indices: 53651--53735 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 35
53641 TCGATGTTTA
*
53651 TTGCTCGTTAAGCTCGATGCTCGTTGTTTGCCTCG
1 TTGCTCGTTAAGCTCGATGCTCGTTGCTTGCCTCG
**
53686 TTGCTCGTTAAGCTCGATGCTCGTTGCTTGTTTCG
1 TTGCTCGTTAAGCTCGATGCTCGTTGCTTGCCTCG
53721 TTGCTCGTTAAGCTC
1 TTGCTCGTTAAGCTC
53736 ATTGAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.41
Consensus pattern (35 bp):
TTGCTCGTTAAGCTCGATGCTCGTTGCTTGCCTCG
Found at i:67042 original size:27 final size:27
Alignment explanation
Indices: 67012--67073 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
67002 TCAATTAAAA
*
67012 TTTATAATAATATATATAAATTGAG-TT
1 TTTATAATAATAAATA-AAATTGAGATT
*
67039 TTTATAA-AA-AAATAAAATTTAGATT
1 TTTATAATAATAAATAAAATTGAGATT
67064 TTTAT-ATAAT
1 TTTATAATAAT
67074 CATTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 8 0.27
25 13 0.43
26 2 0.07
27 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTATAATAATAAATAAAATTGAGATT
Found at i:67085 original size:18 final size:21
Alignment explanation
Indices: 67061--67141 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 21
67051 TAAAATTTAG
67061 ATTTTTATATAATCATT-A-T
1 ATTTTTATATAATCATTAATT
*
67080 -TTTTTATATAATAATTAATT
1 ATTTTTATATAATCATTAATT
*
67100 ATTTTTAATATAATCAATAATTTT
1 ATTTTT-ATATAATCATTAA--TT
* *
67124 ATTTTTATTTAATAATTA
1 ATTTTTATATAATCATTA
67142 TATATAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
18 15 0.30
19 1 0.02
20 1 0.02
21 5 0.10
22 11 0.22
23 9 0.18
24 8 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTTATATAATCATTAATT
Found at i:67101 original size:22 final size:22
Alignment explanation
Indices: 67075--67141 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
67065 TTATATAATC
67075 ATTATTTTTTATATAATAATTA
1 ATTATTTTTTATATAATAATTA
*
67097 ATTATTTTTAATATAATCAA-TA
1 ATTATTTTTTATATAAT-AATTA
* *
67119 ATTTTATTTTTATTTAATAATTA
1 ATTAT-TTTTTATATAATAATTA
67142 TATATAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 24 0.63
23 14 0.37
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTTTTTATATAATAATTA
Found at i:67136 original size:23 final size:25
Alignment explanation
Indices: 67069--67130 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
67059 AGATTTTTAT
*
67069 ATAATCATTATTTTT--TAT-AT-A
1 ATAATTATTATTTTTAATATAATCA
67090 ATAATTAATTATTTTTAATATAATCA
1 ATAATT-ATTATTTTTAATATAATCA
67116 ATAATT-TTATTTTTA
1 ATAATTATTATTTTTA
67131 TTTAATAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
21 5 0.14
22 9 0.26
24 12 0.34
25 2 0.06
26 7 0.20
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
ATAATTATTATTTTTAATATAATCA
Found at i:67561 original size:2 final size:2
Alignment explanation
Indices: 67554--67604 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
67544 ATTTAATGAT
67554 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
67596 TA TA TA TA T
1 TA TA TA TA T
67605 CATTGTAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67874 original size:20 final size:20
Alignment explanation
Indices: 67846--67890 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
67836 GTATGTTGTA
*
67846 AAATTTCAACATTTTGTATC
1 AAATATCAACATTTTGTATC
67866 AAATATCAACATTTTGTATC
1 AAATATCAACATTTTGTATC
67886 AAATA
1 AAATA
67891 AGGTGGTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (20 bp):
AAATATCAACATTTTGTATC
Found at i:69594 original size:21 final size:22
Alignment explanation
Indices: 69568--69618 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
69558 TACCTAAGAT
*
69568 TATCGATACTCTTGCCT-AGAG
1 TATCGATACTCTCGCCTGAGAG
* *
69589 TATCGATACTCTCGCTTGAGGG
1 TATCGATACTCTCGCCTGAGAG
69611 TATCGATA
1 TATCGATA
69619 TTGCCCCGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (22 bp):
TATCGATACTCTCGCCTGAGAG
Found at i:71833 original size:31 final size:31
Alignment explanation
Indices: 71735--71825 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
71725 CAATTTAAGG
71735 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
71766 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
71797 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
71826 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:72031 original size:21 final size:21
Alignment explanation
Indices: 72005--72046 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
71995 ATTTGAATAT
*
72005 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
72026 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
72047 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:72368 original size:34 final size:32
Alignment explanation
Indices: 72329--72398 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
72319 TTTTGTAAAG
*
72329 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
72363 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
72395 GGGA
1 GGGA
72399 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:81119 original size:23 final size:23
Alignment explanation
Indices: 81093--81141 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
81083 ATAAAGAACC
81093 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAATAT-CCATT
*
81116 AAAATAAAGTCTAAATATCCATT
1 AAAATAAACTCTAAATATCCATT
81139 AAA
1 AAA
81142 CCAACCACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTCTAAATATCCATT
Found at i:84396 original size:20 final size:20
Alignment explanation
Indices: 84371--84414 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
84361 GATAAAAAGT
*
84371 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
**
84391 AAAAGTTAAGGATGAAAGAG
1 AAAAGTTAAAAATGAAAGAG
84411 AAAA
1 AAAA
84415 TAAAAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:84434 original size:26 final size:25
Alignment explanation
Indices: 84357--84436 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
84347 TGAAGAAGAT
*
84357 GAGAGATAAAAAG-TAAAAGTTAAA
1 GAGAAATAAAAAGTTAAAAGTTAAA
* * *
84381 AATGAAATAGAAAAGTT-AAGGATGAAA
1 GA-GAAATA-AAAAGTTAAAAG-TTAAA
84408 GAGAAAATAAAAAGTTAAAAGTTAAA
1 GAG-AAATAAAAAGTTAAAAGTTAAA
84434 GAG
1 GAG
84437 GGAAAAGGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
24 1 0.02
25 5 0.12
26 23 0.53
27 14 0.33
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.17
Consensus pattern (25 bp):
GAGAAATAAAAAGTTAAAAGTTAAA
Found at i:84741 original size:5 final size:5
Alignment explanation
Indices: 84707--84740 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
84697 AATTAATTAC
*
84707 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAG AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
84741 GCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:90300 original size:50 final size:45
Alignment explanation
Indices: 90236--90357 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 45
90226 TTCTTACATT
* *
90236 TTATCCCATAAGCTCATAAGCTTATTTTTTACCAAAATACTTACCA
1 TTATTCCATAAGCTCATAAGCTTATTTTTT-CCAAAATACCTACCA
* ** * *
90282 TTTAAAATTCCATAAGCTCGTAAGCTTATTTTTTTTAATATACCTGCCA
1 -TT---ATTCCATAAGCTCATAAGCTTATTTTTTCCAAAATACCTACCA
90331 TTATTCCATAAGCTCATAAGCTTATTT
1 TTATTCCATAAGCTCATAAGCTTATTT
90358 GCATGGTTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
45 24 0.38
47 2 0.03
48 2 0.03
49 10 0.16
50 26 0.41
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (45 bp):
TTATTCCATAAGCTCATAAGCTTATTTTTTCCAAAATACCTACCA
Found at i:95483 original size:14 final size:14
Alignment explanation
Indices: 95464--95494 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
95454 AACACCCGTA
95464 ACCCGTATATTTAT
1 ACCCGTATATTTAT
95478 ACCCGTATATTTAT
1 ACCCGTATATTTAT
95492 ACC
1 ACC
95495 ACTATCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (14 bp):
ACCCGTATATTTAT
Found at i:95891 original size:47 final size:49
Alignment explanation
Indices: 95780--95897 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 49
95770 ACCTTTTATC
95780 CCATAAGCTCATAAGCTTA--TTTTTACCAAAATACTTACCATTTAAAATT
1 CCATAAGCTCATAAGCTTATTTTTTTACCAAAATACTTACCATTT--AATT
* ** * *
95829 CCATAAGCTCGTAAGCTTATTTTTTTTTCAATATACTTGCCA-TT-ATT
1 CCATAAGCTCATAAGCTTATTTTTTTACCAAAATACTTACCATTTAATT
*
95876 CCGTAAGCTCATAAGCTTATTT
1 CCATAAGCTCATAAGCTTATTT
95898 GCATGGTTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 23 0.38
49 18 0.30
50 2 0.03
51 17 0.28
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (49 bp):
CCATAAGCTCATAAGCTTATTTTTTTACCAAAATACTTACCATTTAATT
Found at i:101008 original size:23 final size:23
Alignment explanation
Indices: 100982--101030 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
100972 ATAAAGAACC
100982 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAATAT-CCATT
*
101005 AAAATAAAGTCTAAATATCCATT
1 AAAATAAACTCTAAATATCCATT
101028 AAA
1 AAA
101031 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTCTAAATATCCATT
Found at i:107890 original size:36 final size:36
Alignment explanation
Indices: 107850--107935 Score: 136
Period size: 36 Copynumber: 2.4 Consensus size: 36
107840 CGGAAGAGAT
* *
107850 GATTCACATCGAACGGAAGGAGGCATAGAAACTTCC
1 GATTCAAATCGAACGGAAGGAAGCATAGAAACTTCC
* *
107886 GATTCAAATCGAACGGAAGGAAGCATCGACACTTCC
1 GATTCAAATCGAACGGAAGGAAGCATAGAAACTTCC
107922 GATTCAAATCGAAC
1 GATTCAAATCGAAC
107936 TGAAAGATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (36 bp):
GATTCAAATCGAACGGAAGGAAGCATAGAAACTTCC
Found at i:109153 original size:35 final size:35
Alignment explanation
Indices: 109104--109309 Score: 268
Period size: 35 Copynumber: 5.8 Consensus size: 35
109094 GAATAAGAAC
109104 AACGAAAGGAAGCATCGGCACTTTCGATTCAAGTG
1 AACGAAAGGAAGCATCGGCACTTTCGATTCAAGTG
* * *
109139 AACGGAAGGAAGCATCGACACTTTCGATTCAAGAAG
1 AACGAAAGGAAGCATCGGCACTTTCGATTCAAG-TG
* *
109175 AATGAAATGAAGCATCGGCACTTTCGATTCAAGTG
1 AACGAAAGGAAGCATCGGCACTTTCGATTCAAGTG
* * *
109210 AACGGAAGGAAGCATCGACACTTTCGATTCAAGAAG
1 AACGAAAGGAAGCATCGGCACTTTCGATTCAAG-TG
**
109246 AACGAAATAAAGCATCGGCACTTTCGATTCAAGTG
1 AACGAAAGGAAGCATCGGCACTTTCGATTCAAGTG
** **
109281 AACGGGAGGAAGCATAAGCACTTTCGATT
1 AACGAAAGGAAGCATCGGCACTTTCGATT
109310 TAATTGCTCA
Statistics
Matches: 145, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
35 85 0.59
36 60 0.41
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (35 bp):
AACGAAAGGAAGCATCGGCACTTTCGATTCAAGTG
Found at i:109191 original size:71 final size:71
Alignment explanation
Indices: 109098--109309 Score: 354
Period size: 71 Copynumber: 3.0 Consensus size: 71
109088 GAAGGTGAAT
* *
109098 AAGAACAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGACACTTT
1 AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGACACTTT
109163 CGATTC
66 CGATTC
*
109169 AAGAAGAATGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGACACTTT
1 AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGACACTTT
109234 CGATTC
66 CGATTC
* * *
109240 AAGAAGAACGAAATAAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCAT-AAGCACTT
1 AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGA-CACTT
109304 TCGATT
65 TCGATT
109310 TAATTGCTCA
Statistics
Matches: 133, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
70 1 0.01
71 132 0.99
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (71 bp):
AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGACACTTT
CGATTC
Found at i:111170 original size:12 final size:12
Alignment explanation
Indices: 111153--111177 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111143 AAAGATAAAG
111153 ATTAAATAAATA
1 ATTAAATAAATA
111165 ATTAAATAAATA
1 ATTAAATAAATA
111177 A
1 A
111178 AATATATTAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAAATA
Found at i:111198 original size:19 final size:17
Alignment explanation
Indices: 111160--111198 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
111150 AAGATTAAAT
*
111160 AAATAATTAAATAAATA
1 AAATAATTAAATAAAGA
111177 AAATATATTAAGATAAAGA
1 AAATA-ATTAA-ATAAAGA
111196 AAA
1 AAA
111199 CTTATGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATAATTAAATAAAGA
Found at i:112067 original size:85 final size:85
Alignment explanation
Indices: 111919--112096 Score: 263
Period size: 85 Copynumber: 2.1 Consensus size: 85
111909 AAAAACAAGC
*
111919 TAAAGATAATTTCTAAAATAATATCTTAAATCCTAATTAAATCACTTAAAACTATTTAAACTAAA
1 TAAA-ATAATTTCTAAAATAATATCCTAAATCCTAATTAAATCACTTAAAACTATTTAAACTAAA
*
111984 GTACCTAAAACAAAGATAAAA
65 ATACCTAAAACAAAGATAAAA
*
112005 TAAAATAATATT-TAAAATAATATCCTAAATCCTAATTGAAAT-AC-TAACATCTATTTAAACTA
1 TAAAATAAT-TTCTAAAATAATATCCTAAATCCTAATT-AAATCACTTAA-AACTATTTAAACTA
112067 AAATACCTAAAACAAAGATAAAA
63 AAATACCTAAAACAAAGATAAAA
*
112090 TATAATA
1 TAAAATA
112097 GTTAAAATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
84 3 0.04
85 72 0.85
86 10 0.12
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.30
Consensus pattern (85 bp):
TAAAATAATTTCTAAAATAATATCCTAAATCCTAATTAAATCACTTAAAACTATTTAAACTAAAA
TACCTAAAACAAAGATAAAA
Found at i:112613 original size:15 final size:15
Alignment explanation
Indices: 112593--112627 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
112583 GACAAAACTA
112593 AGTAAATTTAAAGTG
1 AGTAAATTTAAAGTG
112608 AGTAAATTTAAAGTG
1 AGTAAATTTAAAGTG
112623 AGTAA
1 AGTAA
112628 GATATCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (15 bp):
AGTAAATTTAAAGTG
Found at i:113074 original size:37 final size:35
Alignment explanation
Indices: 112994--113075 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 35
112984 ATTTTCCTTC
* * * *
112994 TTTTTTCTTTCTATGTTCGAAATAGTGAACATTTTT
1 TTTTTT-TTTATATGTTCGAAACAGTGAACACTTTA
113030 TTCTTTTTTTATACTGTTCGAAACAGTGAACAACTTTA
1 TT-TTTTTTTATA-TGTTCGAAACAGTGAAC-ACTTTA
113068 TTTTTTTT
1 TTTTTTTT
113076 CTTCGAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 7 0.18
37 26 0.67
38 6 0.15
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (35 bp):
TTTTTTTTTATATGTTCGAAACAGTGAACACTTTA
Found at i:115977 original size:5 final size:5
Alignment explanation
Indices: 115967--116076 Score: 66
Period size: 5 Copynumber: 21.8 Consensus size: 5
115957 ATAAGAGAAA
* * * *
115967 AAAAT AAAAT AAAAT AAAA- AAATT AAAAT -AAAT AGAAT AATAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*** * *
116015 -TTTT AAAAAT AAAAT GAAAAT AAAA- AGAAAT AAAAA ATAAAT AAATT
1 AAAAT -AAAAT AAAAT -AAAAT AAAAT A-AAAT AAAAT A-AAAT AAAAT
116062 AAAAT GAAAAT AAAA
1 AAAAT -AAAAT AAAA
116077 AGGAATGTGT
Statistics
Matches: 79, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
4 9 0.11
5 54 0.68
6 16 0.20
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:116012 original size:19 final size:20
Alignment explanation
Indices: 115964--116012 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
115954 CTGATAAGAG
115964 AAAAAA-ATAAAATAAAATA
1 AAAAAATATAAAATAAAATA
115983 AAAAAAT-TAAAAT-AAATA
1 AAAAAATATAAAATAAAATA
* *
116001 GAATAATATAAA
1 AAAAAATATAAA
116013 GTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAAATATAAAATAAAATA
Found at i:116036 original size:11 final size:11
Alignment explanation
Indices: 116020--116076 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
116010 AAAGTTTTTA
116020 AAAATAAAATG
1 AAAATAAAATG
*
116031 AAAATAAAAAG
1 AAAATAAAATG
* *
116042 AAATAAAAAATAA
1 AAA-ATAAAAT-G
116055 ATAAATTAAAATG
1 A-AAA-TAAAATG
116068 AAAATAAAA
1 AAAATAAAA
116077 AGGAATGTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 18 0.50
12 8 0.22
13 3 0.08
14 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:116046 original size:21 final size:21
Alignment explanation
Indices: 116021--116078 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 21
116011 AAGTTTTTAA
116021 AAATAAAATGAAAATAAAAAG
1 AAATAAAATGAAAATAAAAAG
*
116042 AAAT--AA--AAAATAAATA-
1 AAATAAAATGAAAATAAAAAG
*
116058 AATTAAAATGAAAATAAAAAG
1 AAATAAAATGAAAATAAAAAG
116079 GAATGTGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
16 3 0.10
17 9 0.31
18 2 0.07
19 2 0.07
20 9 0.31
21 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
AAATAAAATGAAAATAAAAAG
Done.