Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009523.1 Hibiscus syriacus cultivar Beakdansim tig00115804_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: 46072
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1551 original size:17 final size:18
Alignment explanation
Indices: 1521--1554 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1511 GAGAAAATTT
*
1521 ATGGAAAATTATGTAGGG
1 ATGGAAAATAATGTAGGG
1539 ATGG-AAATAATGTAGG
1 ATGGAAAATAATGTAGG
1555 AAGTATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.26
Consensus pattern (18 bp):
ATGGAAAATAATGTAGGG
Found at i:3113 original size:21 final size:22
Alignment explanation
Indices: 3087--3140 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
3077 TAGGTCCTTA
3087 TATTTTATGTTTAT-TTTAATT
1 TATTTTATGTTTATCTTTAATT
*
3108 TATTTTATG-TTATCTTTATTT
1 TATTTTATGTTTATCTTTAATT
3129 TATTATT-TGTTT
1 TATT-TTATGTTT
3141 TATTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.14
21 21 0.72
22 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (22 bp):
TATTTTATGTTTATCTTTAATT
Found at i:3126 original size:6 final size:5
Alignment explanation
Indices: 3087--3152 Score: 60
Period size: 5 Copynumber: 12.2 Consensus size: 5
3077 TAGGTCCTTA
* *
3087 TATTT TATGTT TATTT TAATT TATTT TATGT TATCTT TATTT TATTATT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TAT-TT TATTT TA-T-TT
*
3136 TGTTT TATTAT TATTT T
1 TATTT TATT-T TATTT T
3153 TTAATTGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 31 0.62
6 16 0.32
7 3 0.06
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:7143 original size:13 final size:13
Alignment explanation
Indices: 7125--7151 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7115 TCCATTTTTT
7125 GTGACAGTGACGG
1 GTGACAGTGACGG
7138 GTGACAGTGACGG
1 GTGACAGTGACGG
7151 G
1 G
7152 ATACACTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.48, T:0.15
Consensus pattern (13 bp):
GTGACAGTGACGG
Found at i:9373 original size:55 final size:55
Alignment explanation
Indices: 9286--9710 Score: 549
Period size: 55 Copynumber: 7.7 Consensus size: 55
9276 AATGGGTTCA
** * * *
9286 CTCCCTATTTCTTTCAGCCAGTAT-AGAACTCGAATAATCTTCAATAATCGTGTTTG
1 CTCCCTA-TTCTTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTG
* *
9342 CTCTCTATT-TCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCT-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
*
9397 CTCCCTATT-TCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCT-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
*
9452 CTCCCTATT-TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATTGTGTCTG
1 CTCCCTATTCT-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* * * * * *
9507 CTCCCTATTCTTTCAGAGAGTATGAGTCTTGAACAATCTTCGATAATTGTGTCTG
1 CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
9562 CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATTGTGTCTG
1 CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
9617 CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATATTCAACAATCGTGTCCG
1 CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
* * *
9672 TTCCCTATTC-TTCAGGGAGTAT-AGAACTC-AAAAATCTTC
1 CTCCCTATTCTTTCAGAGAGTATAAG-ACTCGAACAATCTTC
9711 TTCTTACGGG
Statistics
Matches: 339, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
53 10 0.03
54 16 0.05
55 304 0.90
56 9 0.03
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (55 bp):
CTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
Found at i:9737 original size:54 final size:54
Alignment explanation
Indices: 9679--10465 Score: 1075
Period size: 54 Copynumber: 14.6 Consensus size: 54
9669 CCGTTCCCTA
* * *
9679 TTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCCCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * *
9733 TTCTTCAGGAAGTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCCCTCCCCCT
1 TTCTTCAGGAAGTATAGAACTC-GAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
9788 TTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTCACTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
9842 TTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
9896 TTCTTCAGGAAGTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTC-GAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* **
9951 TTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
10005 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
10059 TTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTCGCTACCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * *
10113 TTCTTCAGAAAGTATAGAACTCGAAAATATTTTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * * *
10167 TTCTTTAGGAAATATAGACCTCGAAAATCTTCTTCTTACAGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * * ** **
10221 TTTTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTTTCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* ** * *
10275 TTCTTCAGGGAGTATAGAACTCGAAAA---TCTTCAAACGAGTTTGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
**** * *
10326 TTCTTCA-GATAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTTGCTCGCTCT
1 TTCTTCAGGA-AGTATAGAACTCGAA-AATCTTCTTCTTACGGGTTCGCTCCCTCT
* **
10381 TTCTTCAGGGAGTATAGAACTCGAAAA---TCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
10432 TTCTTCAGGGAGTATAGAACTCGAAAATCTTCTT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTT
10466 TTGCTTCATT
Statistics
Matches: 659, Mismatches: 63, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.00
51 89 0.14
52 2 0.00
54 419 0.64
55 147 0.22
56 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (54 bp):
TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
Found at i:9861 original size:163 final size:161
Alignment explanation
Indices: 9679--10465 Score: 1046
Period size: 163 Copynumber: 4.9 Consensus size: 161
9669 CCGTTCCCTA
* *
9679 TTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCCCTCCCTCTTTCTTCAGGAA
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
* * *
9744 GTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCCCTCCCCCTTTCTTCAGGAAGTATAGAACT
66 GTATAGAACTC-GAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
** *
9809 CGAGAATCTTCTTCTTACGGGTTCACTCCCTCT
130 CGA-AATCTTCTTCAAACGGGTTCGCTCCCTCT
* * *
9842 TTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
*
9907 GTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
66 GTATAGAACTC-GAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACT
9972 CGAACATCTTCTTCAAACGGGTTCGCTCCCTCT
130 CGAA-ATCTTCTTCAAACGGGTTCGCTCCCTCT
10005 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
* * *
10070 GTATAGAACTCGAGAATCTTCTTCTTACGGGTTCGCTACCTCTTTCTTCAGAAAGTATAGAACTC
66 GTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC
* * **
10135 GAAAATATTTTTCTTACGGGTTCGCTCCCTCT
131 G-AAATCTTCTTCAAACGGGTTCGCTCCCTCT
* * * * * * *
10167 TTCTTTAGGAAATATAGACCTCGAAAATCTTCTTCTTACAGGTTCGCTCCCTCTTTTTTCAGGGA
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
* ** ** *
10232 GTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTTTCTCTTTCTTCAGGGAGTATAGAACTC
66 GTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC
* * *
10297 GAAA--ATCTTCAAACGAGTTTGCTCCCTCT
131 GAAATCTTCTTCAAACGGGTTCGCTCCCTCT
* **** * *
10326 TTCTTCA-GATAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTTGCTCGCTCTTTCTTCAGG
1 TTCTTCAGGA-AGTATAGAACTC-AAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGG
* ** *
10390 GAGTATAGAACTCGAAAA---TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAAC
64 AAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
10452 TCGAAAATCTTCTT
129 TCG-AAATCTTCTT
10466 TTGCTTCATT
Statistics
Matches: 560, Mismatches: 57, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
157 45 0.08
158 5 0.01
159 35 0.06
160 52 0.09
161 3 0.01
162 192 0.34
163 228 0.41
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (161 bp):
TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAA
GTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC
GAAATCTTCTTCAAACGGGTTCGCTCCCTCT
Found at i:12447 original size:124 final size:125
Alignment explanation
Indices: 12221--12453 Score: 317
Period size: 124 Copynumber: 1.9 Consensus size: 125
12211 CGCAACATCA
* * *
12221 TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACATATCAGATTGTAAGGCTTACTCTTAATGC
1 TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACATCAAATTGTAAGGCTCACTCTTAATGC
* * *
12286 CTTCTTGGTTTAAATCTTGTCCTCTCAATATGATGTGGGTTCAGCCATTCCCCATCAGTG
66 CTCCTTGGTCTAAATCTTGTCCTCTCAACATGATGTGGGTTCAGCCATTCCCCATCAGTG
* * ** * * *
12346 TCTTA-ACTGGTACGGGCCTTCAAAATGCCTCGTCACCTCAAATTGTAAGGCTCATTCTTCATGC
1 TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACATCAAATTGTAAGGCTCACTCTTAATGC
*
12410 CTCCTTGGTCTGAATCTTG-CCATCTCAACATGATGTGGGTTCAG
66 CTCCTTGGTCTAAATCTTGTCC-TCTCAACATGATGTGGGTTCAG
12454 TCGTGCCCCA
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
123 2 0.02
124 86 0.92
125 5 0.05
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (125 bp):
TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACATCAAATTGTAAGGCTCACTCTTAATGC
CTCCTTGGTCTAAATCTTGTCCTCTCAACATGATGTGGGTTCAGCCATTCCCCATCAGTG
Found at i:13780 original size:12 final size:12
Alignment explanation
Indices: 13763--13810 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
13753 TCCAATTTTT
13763 TTCTTTTCTTTA
1 TTCTTTTCTTTA
13775 TTCTTTTCTTT-
1 TTCTTTTCTTTA
**
13786 TTCTCTTTCTACA
1 TTCT-TTTCTTTA
13799 TTTCTTTTCTTT
1 -TTCTTTTCTTT
13811 CTCTTCATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.14
12 16 0.55
13 5 0.17
14 4 0.14
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTTTCTTTA
Found at i:16064 original size:7 final size:7
Alignment explanation
Indices: 16052--16083 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
16042 AACTACATGC
16052 AATGCAA
1 AATGCAA
16059 AATGCAA
1 AATGCAA
16066 AATGC-A
1 AATGCAA
16072 AATGC-A
1 AATGCAA
16078 AATGCA
1 AATGCA
16084 CGAGGTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
AATGCAA
Found at i:16354 original size:21 final size:21
Alignment explanation
Indices: 16330--16384 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
16320 CAATGAGAAG
16330 TGGTCTTCAT-GTCTTTATGAA
1 TGGTCTTC-TCGTCTTTATGAA
16351 TGGTCTTCTCGTCTTTATGAA
1 TGGTCTTCTCGTCTTTATGAA
*
16372 TGATCTTCTCGTC
1 TGGTCTTCTCGTC
16385 CTTGGTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTTATGAA
Found at i:18191 original size:13 final size:13
Alignment explanation
Indices: 18173--18199 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18163 TCCATTTTTT
18173 GTGACAGTGACGG
1 GTGACAGTGACGG
18186 GTGACAGTGACGG
1 GTGACAGTGACGG
18199 G
1 G
18200 ATACACTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.48, T:0.15
Consensus pattern (13 bp):
GTGACAGTGACGG
Found at i:22728 original size:24 final size:25
Alignment explanation
Indices: 22687--22733 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
22677 AACTCAAAAA
22687 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
22712 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
22734 GAAAGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:23448 original size:16 final size:15
Alignment explanation
Indices: 23390--23448 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 15
23380 AAATACGTAA
23390 AAAT-AAAAAA-AAT
1 AAATAAAAAAATAAT
23403 AAATAAAAATATATAAT
1 AAATAAAAA-A-ATAAT
*
23420 TAATAAAATAAATAAT
1 AAATAAAA-AAATAAT
*
23436 GAATCAAAAAAAT
1 AAAT-AAAAAAAT
23449 TATATTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 1 0.03
16 13 0.34
17 15 0.39
18 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAAAAAAATAAT
Found at i:24482 original size:29 final size:29
Alignment explanation
Indices: 24437--24772 Score: 280
Period size: 30 Copynumber: 11.6 Consensus size: 29
24427 TTAATTTTAC
24437 ATCTTAACATTAAAAATATATTTTATTCTT
1 ATCTTAAC-TTAAAAATATATTTTATTCTT
24467 ATCTTAACTTAAAAATATATTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
24496 ATTTTAACTTAAAAATATATTTTAGTCTTT
1 ATCTTAACTTAAAAATATATTTTATTC-TT
*
24526 ATCTTAACTTAAAAAATATATTTTATTGTT
1 ATCTTAACTT-AAAAATATATTTTATTCTT
* * * *
24556 ATCTTAACTTATTACATAAATTATATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * * *
24586 AACTTTAA-TTATTAAATATATTCTATTTTT
1 ATC-TTAACTTA-AAAATATATTTTATTCTT
* * * * *
24616 A-CCTAAATTATTAAATATAATTAATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * *
24645 ATTTTAAATTAAAACATATTTTTTATTCTT
1 ATCTTAACTTAAAA-ATATATTTTATTCTT
24675 ATCTTAACTTAAAAATATA---T-TT-TT
1 ATCTTAACTTAAAAATATATTTTATTCTT
*
24699 ATTTTAAC-TAAAAA-ATATTTT-TT-TT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* * *
24724 ATCTTAACTACAAAAAATATATTATATTTTT
1 ATCTTAACT--TAAAAATATATTTTATTCTT
* *
24755 ATCTTAAATTTAAAATAT
1 ATCTTAACTTAAAAATAT
24773 TACTAGAATA
Statistics
Matches: 254, Mismatches: 36, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
22 3 0.01
23 6 0.02
24 9 0.04
25 14 0.06
26 1 0.00
28 8 0.03
29 86 0.34
30 98 0.39
31 29 0.11
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:24702 original size:89 final size:89
Alignment explanation
Indices: 24448--24703 Score: 284
Period size: 89 Copynumber: 2.9 Consensus size: 89
24438 TCTTAACATT
*
24448 AAAAATATATTTTATTCTTATCTTAACTTAAAA-ATATATTTTATTCTTATTTTAACTTAAAAAT
1 AAAAATATATTTTATTCTTATCTTAACTTAAAACATATATTTTATTCTTATCTTAACTTAAAAAT
* * *
24512 ATATTTTAGTCTTTATCTTAACTTA
66 ATATTTTA-TTTTTATCCTAAATTA
* ** * * * *
24537 AAAAATATATTTTATTGTTATCTTAACTTATTACATAAATTATATTCTTAACTTTAA-TTATTAA
1 AAAAATATATTTTATTCTTATCTTAACTTAAAACATATATTTTATTCTTATC-TTAACTTA-AAA
*
24601 ATATATTCTATTTTTA-CCTAAATTA
64 ATATATTTTATTTTTATCCTAAATTA
** * * * * *
24626 TTAAATATAATTAATTCTTATTTTAAATTAAAACATATTTTTTATTCTTATCTTAACTTAAAAAT
1 AAAAATATATTTTATTCTTATCTTAACTTAAAACATATATTTTATTCTTATCTTAACTTAAAAAT
24691 ATATTTTTATTTT
66 ATA-TTTTATTTT
24704 AACTAAAAAA
Statistics
Matches: 135, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
88 11 0.08
89 87 0.64
90 22 0.16
91 15 0.11
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (89 bp):
AAAAATATATTTTATTCTTATCTTAACTTAAAACATATATTTTATTCTTATCTTAACTTAAAAAT
ATATTTTATTTTTATCCTAAATTA
Found at i:24722 original size:25 final size:24
Alignment explanation
Indices: 24668--24746 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
24658 ACATATTTTT
* *
24668 TATTCTTATCTTAACTTAAAAATA
1 TATTTTTATCTTAACTAAAAAATA
*
24692 TATTTTTATTTTAACTAAAAAATA
1 TATTTTTATCTTAACTAAAAAATA
*
24716 TTTTTTTTATCTTAACTACAAAAAATA
1 -TATTTTTATCTTAACT--AAAAAATA
24743 TATT
1 TATT
24747 ATATTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.46
25 14 0.30
26 3 0.07
27 8 0.17
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTTTTATCTTAACTAAAAAATA
Found at i:24868 original size:29 final size:29
Alignment explanation
Indices: 24777--24884 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 29
24767 AAATATTACT
*
24777 AGAATAAAATATAAATATTTAAGTT-AAA-TA
1 AGAATAAAATAT--ATTTTTAA-TTAAAAGTA
24807 AGAATAAATTATATATTTTT-ATTAAAAGTA
1 AGAATAAA--ATATATTTTTAATTAAAAGTA
* *
24837 AGATTTAAATATATTTTTAAATTAAAA-TA
1 AGAATAAAATATATTTTT-AATTAAAAGTA
24866 AGAATAAAATATATTTTTA
1 AGAATAAAATATATTTTTA
24885 GGTTACGAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
28 13 0.19
29 22 0.33
30 28 0.42
32 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (29 bp):
AGAATAAAATATATTTTTAATTAAAAGTA
Found at i:24897 original size:29 final size:30
Alignment explanation
Indices: 24843--24912 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
24833 AGTAAGATTT
*
24843 AAATATATTTTTAAATTAAAATAAG-AATA
1 AAATATATTTTTAAATTAAAATAAGAAAGA
** *
24872 AAATATATTTTTAGGTTACGAA-AAGAAAAGA
1 AAATATATTTTTAAATTA-AAATAAG-AAAGA
24903 AAATATATTT
1 AAATATATTT
24913 AATAAGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 19 0.56
30 2 0.06
31 13 0.38
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (30 bp):
AAATATATTTTTAAATTAAAATAAGAAAGA
Found at i:29755 original size:31 final size:32
Alignment explanation
Indices: 29717--29793 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
29707 AGAATGACCT
29717 GAACCCGAATTGAATC-GA-AAATATGATACCC
1 GAACCCGAATTGAATCTGACAAATATGA-ACCC
* * **
29748 GAACCCGAACTGCATCTGACTGATATGAACCC
1 GAACCCGAATTGAATCTGACAAATATGAACCC
29780 GAACCCGAGATTGA
1 GAACCCGA-ATTGA
29794 CCTGGTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 14 0.38
32 14 0.38
33 9 0.24
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (32 bp):
GAACCCGAATTGAATCTGACAAATATGAACCC
Found at i:29843 original size:16 final size:16
Alignment explanation
Indices: 29822--29856 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
29812 TTATCCGAAT
29822 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACC
*
29838 TGTTTTTAACCTGACC
1 TGTTTTCAACCTGACC
29854 TGT
1 TGT
29857 AAATGATCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (16 bp):
TGTTTTCAACCTGACC
Found at i:29897 original size:16 final size:15
Alignment explanation
Indices: 29878--29928 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 15
29868 CTTGTTAATG
29878 ACCTGATCTGATATTT
1 ACCTGA-CTGATATTT
29894 ACCTGACTTGATATTT
1 ACCTGAC-TGATATTT
*
29910 ACCTGACTTATATATT
1 ACCTGACTGATAT-TT
29926 ACC
1 ACC
29929 ATGGACGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 6 0.19
16 26 0.81
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (15 bp):
ACCTGACTGATATTT
Found at i:30753 original size:20 final size:19
Alignment explanation
Indices: 30716--30762 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
30706 TAGTAGTACA
30716 TGCATATTA--ATTTCATT
1 TGCATATTAGTATTTCATT
*
30733 TGCATAATTAGTATTTTATT
1 TGCAT-ATTAGTATTTCATT
30753 TGCATATTAG
1 TGCATATTAG
30763 GTTAATTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 5 0.19
20 12 0.46
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (19 bp):
TGCATATTAGTATTTCATT
Found at i:31035 original size:15 final size:15
Alignment explanation
Indices: 31015--31051 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
31005 TAATTTACTT
31015 TATATAGTTTATATA
1 TATATAGTTTATATA
31030 TATATAGTTTATATA
1 TATATAGTTTATATA
31045 TACTATA
1 TA-TATA
31052 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:31316 original size:2 final size:2
Alignment explanation
Indices: 31309--31335 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31299 ACATACATAT
31309 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
31336 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31340 original size:2 final size:2
Alignment explanation
Indices: 31335--31360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31325 ACACACACAC
31335 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31361 TAAAAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31580 original size:18 final size:20
Alignment explanation
Indices: 31567--31645 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
31557 AAATTTTCTA
31567 TTCCCTCTAAATTTTCCAAT
1 TTCCCTCTAAATTTTCCAAT
31587 TTCCCTCTAAA--TTCACAAT
1 TTCCCTCTAAATTTTC-CAAT
* * * *
31606 TT-CC-ATATATTCTCAAAAT
1 TTCCCTCTAAATTTTC-CAAT
*
31625 TTCCCTCTAAATTTGCCAAT
1 TTCCCTCTAAATTTTCCAAT
31645 T
1 T
31646 CCCACCTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
17 3 0.07
18 5 0.11
19 14 0.31
20 17 0.38
21 6 0.13
ACGTcount: A:0.29, C:0.28, G:0.01, T:0.42
Consensus pattern (20 bp):
TTCCCTCTAAATTTTCCAAT
Found at i:31607 original size:19 final size:19
Alignment explanation
Indices: 31567--31637 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
31557 AAATTTTCTA
31567 TTCCCTCTAAATTTTC-CAAT
1 TTCCCTCTAAA--TTCACAAT
31587 TTCCCTCTAAATTCACAAT
1 TTCCCTCTAAATTCACAAT
* * * *
31606 TTCCATAT-ATTCTCAAAAT
1 TTCCCTCTAAAT-TCACAAT
31625 TTCCCTCTAAATT
1 TTCCCTCTAAATT
31638 TGCCAATTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
18 5 0.12
19 23 0.56
20 13 0.32
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCCCTCTAAATTCACAAT
Found at i:31700 original size:2 final size:2
Alignment explanation
Indices: 31695--31895 Score: 100
Period size: 2 Copynumber: 102.0 Consensus size: 2
31685 TAAACTCATG
* * * * * *
31695 TA TA TA TA TA TA TA TA TA TT TA TA AA TCG T- TA T- TA AA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* * *
31736 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
31779 TA GTT TA TA TA TA TA TA TA TA GT- TCA CA TA TA TA GT- TCA TA TA
1 TA -TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA -TA T-A TA TA
* * * *
31822 AA CA TA -A TT TA TA TA TA TA TG T- TA TA -A TA -A T- 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
* *
31859 GTT TA TA -A TA TA AA TA T- 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
31896 GTTGTTTTAA
Statistics
Matches: 153, Mismatches: 27, Indels: 38
0.70 0.12 0.17
Matches are distributed among these distances:
1 11 0.07
2 135 0.88
3 7 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31837 original size:49 final size:47
Alignment explanation
Indices: 31735--31895 Score: 115
Period size: 47 Copynumber: 3.4 Consensus size: 47
31725 TATTAAATTT
* * **
31735 TTATATATATATATA-TATA-T-ATATATATAGTTTATATATTTTTATA
1 TTATATATATATATATTATATTAAT-TATATAGTTCATA-ATATAAATA
31781 GTT-TATATATATATA-TATAGTTCACA-TATATAGTTCAT-ATA-AACATAA
1 -TTATATATATATATATTATA-TT-A-ATTATATAGTTCATAATATAA-AT-A
* * *
31829 TT-TATATATATATGTTATAATAATTATATAGTTTATAATATAAATA
1 TTATATATATATATATTATATTAATTATATAGTTCATAATATAAATA
31875 TTATATATATATATATATATA
1 TTATATATATATATAT-TATA
31896 GTTGTTTTAA
Statistics
Matches: 93, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
45 1 0.01
46 31 0.33
47 37 0.40
48 12 0.13
49 11 0.12
51 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (47 bp):
TTATATATATATATATTATATTAATTATATAGTTCATAATATAAATA
Found at i:32040 original size:85 final size:85
Alignment explanation
Indices: 31877--32043 Score: 316
Period size: 85 Copynumber: 2.0 Consensus size: 85
31867 TATAAATATT
* *
31877 ATATATATATATATATATAGTTGTTTTAATTTTTTTCTTAACTTTTGAAATGAATGCAATTTTTT
1 ATATATATATATATATATAGTTGTTTTAATTTTTTTCTCAACTTTTGAAATGAATGCAAATTTTT
31942 CATTTTATAATATTTTTATA
66 CATTTTATAATATTTTTATA
31962 ATATATATATATATATATAGTTGTTTTAATTTTTTTCTCAACTTTTGAAATGAATGCAAATTTTT
1 ATATATATATATATATATAGTTGTTTTAATTTTTTTCTCAACTTTTGAAATGAATGCAAATTTTT
32027 CATTTTATAATATTTTT
66 CATTTTATAATATTTTT
32044 CATATTTGAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (85 bp):
ATATATATATATATATATAGTTGTTTTAATTTTTTTCTCAACTTTTGAAATGAATGCAAATTTTT
CATTTTATAATATTTTTATA
Found at i:32733 original size:214 final size:215
Alignment explanation
Indices: 32063--32756 Score: 1205
Period size: 215 Copynumber: 3.2 Consensus size: 215
32053 TCCCTTCGTA
* *
32063 TTGTTTAATTTACTTAAATTTTTATTTATAATTTCATATTT-TTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
*
32127 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGCCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
32192 TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAGTTATTTCGATT
131 TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATT
32257 TGATCCCTCATCAATGTGTG
196 TGATCCCTCATCAATGTGTG
* *
32277 TTCTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAATTTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
* *
32342 ATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* * *
32407 TAAATGGGTATACTTTATTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTTGATT
131 TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATT
32472 TGATCCCTCATCAATGTGTG
196 TGATCCCTCATCAATGTGTG
* * *
32492 TTATTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGACCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
32557 ATTTGCATCTAAAATTGACCCATACTTATTACTTA-TT-TATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
*
32620 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAGTTTAAAATTATTTAGAT
131 TAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGAT
32685 TTGATCCCTCATCAATGTGTG
195 TTGATCCCTCATCAATGTGTG
*
32706 TTGTTTAATTTATTTAAATTTTTATTTGTAATTCCATATTTGTTCAATTTA
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
32757 ATTCTTAAAT
Statistics
Matches: 454, Mismatches: 24, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
213 44 0.10
214 150 0.33
215 260 0.57
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.50
Consensus pattern (215 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATT
TGATCCCTCATCAATGTGTG
Found at i:39332 original size:8 final size:8
Alignment explanation
Indices: 39319--39385 Score: 53
Period size: 8 Copynumber: 7.8 Consensus size: 8
39309 AAATAAATAA
*
39319 AGAAAAAC
1 AGAAAAAG
39327 AGAAAAAAG
1 AG-AAAAAG
39336 AGAAAAAG
1 AGAAAAAG
*
39344 AGAAAAAA
1 AGAAAAAG
*
39352 AGAAAGAGAA
1 AGAAA-A-AG
*
39362 AGAAAAAA
1 AGAAAAAG
39370 AGAAAGAAG
1 AGAAA-AAG
39379 AAGAAAA
1 -AGAAAA
39386 CCAATCAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
8 27 0.53
9 12 0.24
10 12 0.24
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (8 bp):
AGAAAAAG
Found at i:39339 original size:17 final size:16
Alignment explanation
Indices: 39269--39385 Score: 92
Period size: 17 Copynumber: 7.0 Consensus size: 16
39259 ACACAGGGAG
*
39269 AAAGAAAAAAATAGAAA
1 AAAGAAAAAAAGA-AAA
* * * *
39286 AAATATAAAAA-TAAG
1 AAAGAAAAAAAGAAAA
* *
39301 AAAGAAAAAAATAAAT
1 AAAGAAAAAAAGAAAA
*
39317 AAAGAAAAACAGAAAA
1 AAAGAAAAAAAGAAAA
*
39333 AAGAGAAAAAGAGAAAA
1 AA-AGAAAAAAAGAAAA
39350 AAAGAAAGAGAAAGAAAA
1 AAAGAAA-A-AAAGAAAA
39368 AAAGAAAGAAGAAGAAAA
1 AAAGAAA-AA-AAGAAAA
39386 CCAATCAAAC
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
15 11 0.13
16 22 0.27
17 26 0.32
18 23 0.28
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAGAAAAAAAGAAAA
Found at i:39350 original size:26 final size:26
Alignment explanation
Indices: 39281--39384 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 26
39271 AGAAAAAAAT
* *
39281 AGAAAAAATATAAAAATAAGAAAGAAAA
1 AGAAAAAA-AGAAAAA-AAGAAAGAGAA
* *
39309 AAATAAATAAAGAAAAACAGAAA-A-AA
1 AGA-AAA-AAAGAAAAAAAGAAAGAGAA
*
39335 GAGAAAAAGAGAAAAAAAGAAAGAGAA
1 -AGAAAAAAAGAAAAAAAGAAAGAGAA
39362 AGAAAAAAAGAAAGAAGAAGAAA
1 AGAAAAAAAGAAA-AA-AAGAAA
39385 ACCAATCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
25 13 0.21
26 18 0.29
27 7 0.11
28 13 0.21
29 9 0.15
30 2 0.03
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (26 bp):
AGAAAAAAAGAAAAAAAGAAAGAGAA
Found at i:39351 original size:55 final size:55
Alignment explanation
Indices: 39274--39377 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 55
39264 GGGAGAAAGA
* * * *
39274 AAAAAATAGAAAAAATATAAAAATAAGAAAGA-AAA-AAATAAATAAAGAAAAACAG
1 AAAAAAGAGAAAAAA-GTAAAAA-AAGAAAGAGAAAGAAAAAAAGAAAGAAAAACAG
39329 AAAAAAGAGAAAAAGAG-AAAAAAAGAAAGAGAAAGAAAAAAAGAAAGAA
1 AAAAAAGAGAAAAA-AGTAAAAAAAGAAAGAGAAAGAAAAAAAGAAAGAA
39378 GAAGAAAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
53 8 0.19
54 8 0.19
55 25 0.60
56 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.06
Consensus pattern (55 bp):
AAAAAAGAGAAAAAAGTAAAAAAAGAAAGAGAAAGAAAAAAAGAAAGAAAAACAG
Found at i:39359 original size:14 final size:14
Alignment explanation
Indices: 39266--39372 Score: 63
Period size: 15 Copynumber: 7.1 Consensus size: 14
39256 ATAACACAGG
39266 GAGAAAGAAAAAAA
1 GAGAAAGAAAAAAA
* *
39280 TAGAAAAAATATAAAAA
1 GAG-AAAGA-A-AAAAA
*
39297 TAAGAAAGAAAAAAATA
1 -GAGAAAG-AAAAAA-A
* * *
39314 AATAAAGAAAAACA
1 GAGAAAGAAAAAAA
* *
39328 GAAAAAAGAGAAAAA
1 G-AGAAAGAAAAAAA
39343 GAGAAA-AAAAGAAA
1 GAGAAAGAAAA-AAA
39357 GAGAAAGAAAAAAA
1 GAGAAAGAAAAAAA
39371 GA
1 GA
39373 AAGAAGAAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
13 3 0.04
14 21 0.29
15 24 0.33
16 11 0.15
17 10 0.14
18 3 0.04
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.06
Consensus pattern (14 bp):
GAGAAAGAAAAAAA
Found at i:39360 original size:22 final size:18
Alignment explanation
Indices: 39266--39385 Score: 74
Period size: 18 Copynumber: 6.6 Consensus size: 18
39256 ATAACACAGG
39266 GAGAAAGAAAAAAATAGAAA
1 GAGAAAG-AAAAAA-AGAAA
*
39286 -A-AATATAAAAATAAGAAA
1 GAGAA-AGAAAAA-AAGAAA
* *
39304 GAAAAAAATAAATAAAGAAA
1 GAGAAAGA-AAA-AAAGAAA
*
39324 -A-ACAGAAAAAAGAGAAA
1 GAGAAAGAAAAAA-AGAAA
*
39341 -A-AGAGAAAAAAAGAAA
1 GAGAAAGAAAAAAAGAAA
39357 GAGAAAGAAAAAAAGAAA
1 GAGAAAGAAAAAAAGAAA
39375 GA-AGAAGAAAA
1 GAGA-AAGAAAA
39386 CCAATCAAAC
Statistics
Matches: 84, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
16 7 0.08
17 20 0.24
18 38 0.45
19 7 0.08
20 11 0.13
21 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.05
Consensus pattern (18 bp):
GAGAAAGAAAAAAAGAAA
Found at i:39382 original size:10 final size:9
Alignment explanation
Indices: 39330--39385 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 9
39320 GAAAAACAGA
39330 AAAAAG-AG
1 AAAAAGAAG
39338 AAAAAG-AG
1 AAAAAGAAG
39346 AAAAA-AAG
1 AAAAAGAAG
*
39354 AAAGAGAAAG
1 AAAAAG-AAG
39364 AAAAA-AAG
1 AAAAAGAAG
39372 AAAGAAGAAG
1 AAA-AAGAAG
39382 AAAA
1 AAAA
39386 CCAATCAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 25 0.61
9 3 0.07
10 13 0.32
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:40049 original size:28 final size:28
Alignment explanation
Indices: 40009--40068 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
39999 CAAAGAATCC
* *
40009 AACCTGAAACACATTACCTCCCC-AGATT
1 AACCCGAAACACATGACCTCCCCAAG-TT
*
40037 AACCCGAAACACATGACCTTCCCAAGTT
1 AACCCGAAACACATGACCTCCCCAAGTT
40065 AACC
1 AACC
40069 TAAGCCTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.37, C:0.37, G:0.08, T:0.18
Consensus pattern (28 bp):
AACCCGAAACACATGACCTCCCCAAGTT
Found at i:40810 original size:173 final size:173
Alignment explanation
Indices: 40521--40863 Score: 553
Period size: 173 Copynumber: 2.0 Consensus size: 173
40511 TTGATCACTT
*
40521 TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTATGTCAATTCGATAACATTGCTG
1 TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTATGTCAATTCGATAACATTACTG
* *
40586 ATTAGTGACACTAGAGTGAAACAATTCGAGATTAAGATTTTGTCATGAAGAGAGCCATGAGTACC
66 ATTAGTGACACCAGAGTGAAACAATTCGAGATTAAGATTTTGGCATGAAGAGAGCCATGAGTACC
*
40651 CACATTGGGGTATTACCTAAACCAGATGTCATTAAGATCACGA
131 CACATTGGGGCATTACCTAAACCAGATGTCATTAAGATCACGA
* * * * *
40694 TTTAAGTGTTCATTTGTTTATGGCATCGTGAAGAGAAGCCCT-TAGTCTATTTGATAACATTACT
1 TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTAT-GTCAATTCGATAACATTACT
* *
40758 GATTAGTGACACCAGAGTGAAACTATTCGAGATTAAGATTTTGGCATGAAGAGAGCCTTGAGTAC
65 GATTAGTGACACCAGAGTGAAACAATTCGAGATTAAGATTTTGGCATGAAGAGAGCCATGAGTAC
* *
40823 CCACATTGGGGCATTATCTAAACCAGATGTCGTTAAGATCA
130 CCACATTGGGGCATTACCTAAACCAGATGTCATTAAGATCA
40864 TGAGATTTAA
Statistics
Matches: 156, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
172 1 0.01
173 155 0.99
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (173 bp):
TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTATGTCAATTCGATAACATTACTG
ATTAGTGACACCAGAGTGAAACAATTCGAGATTAAGATTTTGGCATGAAGAGAGCCATGAGTACC
CACATTGGGGCATTACCTAAACCAGATGTCATTAAGATCACGA
Found at i:41657 original size:41 final size:42
Alignment explanation
Indices: 41598--41680 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
41588 AAGGTTTTCT
* *
41598 TGATGATTAAGTCATTC-GGCCATCAATAAGTCTTTCGAGCA
1 TGATGATTAAATCATTCGGGCCATCAATAAGTCTTTCAAGCA
* * * **
41639 TGATGCTTAAATCCTTCGGGTCATTTATAAGTCTTTCAAGCA
1 TGATGATTAAATCATTCGGGCCATCAATAAGTCTTTCAAGCA
41681 AGAAGATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 14 0.41
42 20 0.59
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (42 bp):
TGATGATTAAATCATTCGGGCCATCAATAAGTCTTTCAAGCA
Found at i:41884 original size:57 final size:57
Alignment explanation
Indices: 41759--41878 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 57
41749 CAAGCCTGAC
* **
41759 TTTCTGGGGTTTCTTGATGATTATCTCCAAAGAATTTTTAAAGAAACTAAGCATAAT
1 TTTCAGGGGTTTCTTGATGACAATCTCCAAAGAATTTTTAAAGAAACTAAGCATAAT
* * * * * * *
41816 TTTTAGGGGTTTCTTGATGACAATTTTCAATGAATTTTTATGAGAAACTAAGCTTGAT
1 TTTCAGGGGTTTCTTGATGACAATCTCCAAAGAATTTTTA-AAGAAACTAAGCATAAT
41874 TTTCA
1 TTTCA
41879 TGGTTTTATT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
57 33 0.65
58 18 0.35
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (57 bp):
TTTCAGGGGTTTCTTGATGACAATCTCCAAAGAATTTTTAAAGAAACTAAGCATAAT
Found at i:42197 original size:42 final size:41
Alignment explanation
Indices: 42151--42270 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
42141 AACAGTTTCT
42151 TGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCA
* * * * *
42193 TGATGCGTAAGTCCTTTGAGCCATTTATAAGTCTTTCGAGTA
1 TGATGAGTAAGTCCTTCGGGCCA-TCATAAGTCTTTCGAGCA
* *
42235 GGATGA-TAAGTCCTTCGGGCCATCCATAAGACTTTC
1 TGATGAGTAAGTCCTTCGGGCCAT-CATAAGTCTTTC
42271 AGGTAGGATT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.02
41 24 0.37
42 38 0.58
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (41 bp):
TGATGAGTAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCA
Found at i:42478 original size:260 final size:261
Alignment explanation
Indices: 41858--42601 Score: 1055
Period size: 263 Copynumber: 2.8 Consensus size: 261
41848 AATTTTTATG
* * * *
41858 AGAAACTAAGCTTGATTTTCATGGTTTTATTAATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
* * ** *
41923 TCGAGCATGATGCTTAAGTCCTTCGGGATATTTATAAGTCTTTCGAGCTAAATGATAAGACCTTC
66 TCGAGCATGATGCGTAAGTCTTTCGGGCCATTTATAAGTCTTTCGAG-TAGATGATAAGACCTTC
* * * * *
41988 GAGCCATCCATAAGACCTTCGGACAAGATGTTTTCAACATTTTTCGTGCTCGATTAATCACATAT
130 GGGCCATCCATAAGACATTCGG-CAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATAT
*
42053 GGAGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATGTAGGGGTTCCTTGATGACAA
194 GGAGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATATAGGGGTTCCTTGATGACAA
*
42118 TTA
259 CTA
** *
42121 AGAAACTAAGCTTGATTTTCAACAGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
* *
42186 TCGAGCATGATGCGTAAGTCCTTT-GAGCCATTTATAAGTCTTTCGAGTAGGATGATAAGTCCTT
66 TCGAGCATGATGCGTAAGT-CTTTCGGGCCATTTATAAGTCTTTCGAGTA-GATGATAAGACCTT
* * * *
42250 CGGGCCATCCATAAGACTTTCAGGTAGGATTTTTTCAACATTTCTGGTACTCGATTAATCACATA
129 CGGGCCATCCATAAGACATTC-GGCAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATA
* * *
42315 TGGAG-T-AATCAGCAATACCTCACTCGAGGGACCAACATAATATATAGGGGTTCCTTGATGACA
193 TGGAGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATATAGGGGTTCCTTGATGACA
42378 ACTA
258 ACTA
42382 AGAAACTAAGC-TGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
* * * * *
42446 TTGAGCATGATGCGTAAGTCTTTCGGGCCATTTATAACTTTTTAGAGCAAGATGATAAGACCTTC
66 TCGAGCATGATGCGTAAGTCTTTCGGGCCATTTATAAGTCTTTCGAG-TAGATGATAAGACCTTC
* * * *
42511 GGGCTATCCATAAGACATTCGGGCAAAATGTTTTCAAAATTTCTGGTACTTGATTAATCACATAT
130 GGGCCATCCATAAGACATTC-GGCAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATAT
*
42576 AGAGTTGAATCAACAACACCTCACTC
194 GGAGTTGAATCAACAACACCTCACTC
42602 TAGGAATCAA
Statistics
Matches: 425, Mismatches: 49, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
259 4 0.01
260 160 0.38
261 69 0.16
262 20 0.05
263 167 0.39
264 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (261 bp):
AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
TCGAGCATGATGCGTAAGTCTTTCGGGCCATTTATAAGTCTTTCGAGTAGATGATAAGACCTTCG
GGCCATCCATAAGACATTCGGCAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATATGG
AGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATATAGGGGTTCCTTGATGACAACT
A
Found at i:43037 original size:38 final size:38
Alignment explanation
Indices: 42995--43073 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
42985 CAACCCAAAT
42995 AAAAACCAAAGCTGGGCCTTAAGCCCAAGATGGACCAA
1 AAAAACCAAAGCTGGGCCTTAAGCCCAAGATGGACCAA
43033 AAAAACCAAAGCTGGGCCTTAAGCCCAAGATGGACCAA
1 AAAAACCAAAGCTGGGCCTTAAGCCCAAGATGGACCAA
43071 AAA
1 AAA
43074 CTAAACTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.10
Consensus pattern (38 bp):
AAAAACCAAAGCTGGGCCTTAAGCCCAAGATGGACCAA
Found at i:43060 original size:19 final size:19
Alignment explanation
Indices: 43000--43060 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
42990 CAAATAAAAA
43000 CCAAAGCTGGGCCTTAAGC
1 CCAAAGCTGGGCCTTAAGC
* * ** **
43019 CC-AAGATGGACCAAAAAAA
1 CCAAAGCTGGGCC-TTAAGC
43038 CCAAAGCTGGGCCTTAAGC
1 CCAAAGCTGGGCCTTAAGC
43057 CCAA
1 CCAA
43061 GATGGACCAA
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 8 0.29
19 12 0.43
20 8 0.29
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11
Consensus pattern (19 bp):
CCAAAGCTGGGCCTTAAGC
Done.