Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003545.1 Hibiscus syriacus cultivar Beakdansim tig00007477_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: 173267
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 2
Found at i:6271 original size:5 final size:5
Alignment explanation
Indices: 6254--6297 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
6244 TCCTAAGTCG
6254 AAGAA AA-AA AAGAA AAGAAAA AAGAA AAGAA AAGAAA AAGAA AA
1 AAGAA AAGAA AAGAA AAG--AA AAGAA AAGAA AAG-AA AAGAA AA
6298 AACATTTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.11
5 21 0.60
6 5 0.14
7 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:6276 original size:12 final size:12
Alignment explanation
Indices: 6259--6299 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
6249 AGTCGAAGAA
6259 AAAAAAGAAAAG
1 AAAAAAGAAAAG
6271 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
6283 AAAAGA-AAAAG
1 AAAAAAGAAAAG
6294 AAAAAA
1 AAAAAA
6300 CATTTAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:6283 original size:17 final size:16
Alignment explanation
Indices: 6257--6297 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6247 TAAGTCGAAG
6257 AAAA-AAAAGAAAAGAA
1 AAAAGAAAAGAAAAG-A
6273 AAAAGAAAAGAAAAGA
1 AAAAGAAAAGAAAAGA
6289 AAAAGAAAA
1 AAAAGAAAA
6298 AACATTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAGA
Found at i:6298 original size:17 final size:16
Alignment explanation
Indices: 6257--6298 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 16
6247 TAAGTCGAAG
6257 AAAAAAAAGAAAAGAA
1 AAAAAAAAGAAAAGAA
6273 AAAAGAAAAGAAAAGAA
1 AAAA-AAAAGAAAAGAA
6290 AAAGAAAAA
1 AAA-AAAAA
6299 ACATTTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAGAA
Found at i:6353 original size:58 final size:59
Alignment explanation
Indices: 6277--6414 Score: 181
Period size: 57 Copynumber: 2.4 Consensus size: 59
6267 AAAGAAAAAA
* * *
6277 GAAAAGAAAAGAAAAAGAAAAAACATTTAGGGTGAAAACCCGAAAGGGCACCCTAAATT
1 GAAAAAAAAAGAAAAAGAAAAAACATTTACGATGAAAACCCGAAAGGGCACCCTAAATT
* * * * * *
6336 G-ATAAAAGAGTAAAAG-AAAAACGTTTACGATGAAAACTCGAAATGGCACCCTAAATT
1 GAAAAAAAAAGAAAAAGAAAAAACATTTACGATGAAAACCCGAAAGGGCACCCTAAATT
6393 GAAAAAAAAAGAAAAAGAAAAA
1 GAAAAAAAAAGAAAAAGAAAAA
6415 TAAGGTAGGT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 37 0.57
58 23 0.35
59 5 0.08
ACGTcount: A:0.57, C:0.12, G:0.18, T:0.13
Consensus pattern (59 bp):
GAAAAAAAAAGAAAAAGAAAAAACATTTACGATGAAAACCCGAAAGGGCACCCTAAATT
Found at i:7527 original size:118 final size:120
Alignment explanation
Indices: 7242--7666 Score: 511
Period size: 124 Copynumber: 3.5 Consensus size: 120
7232 AATTTACTCG
*
7242 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGT
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT-GG-
* ** * * *
7307 CATCCACGATTTTAACTTCATAACGAAGGATATCGTGTCCAC--CAACATTCATCTTT
64 C-TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACAACATCCATCATT
* * *
7363 AGATTGGATTTCAACTTCACGATGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAA-GG-T
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGGCT
* * *
7426 -CACGATTTCAACTTCACGACGAAAGATATGGTGCCCACCAACAACATCCATCCTT
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCA-CAACAACATCCATCATT
* * * *
7481 ATATTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAATGAATGAGC
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATG-G-
** * *
7546 CATCCATTATTTCAACTTCACGATGAAGGATATCGTGCCCATAAGCAACATCCAT-ATCT
64 C-TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAA-CAACATCCATCAT-T
* * *
7605 AGATTGGATTTCAACTTCACGACGAATGATATCAAATTCAAAGCTCAACTTCACAATGAATG
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATG
7667 AGTTTTCAGT
Statistics
Matches: 265, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
115 31 0.12
116 2 0.01
118 65 0.25
119 3 0.01
120 1 0.00
121 58 0.22
123 4 0.02
124 101 0.38
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (120 bp):
AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGGCT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAACAACATCCATCATT
Found at i:9403 original size:9 final size:9
Alignment explanation
Indices: 9389--9482 Score: 72
Period size: 9 Copynumber: 10.4 Consensus size: 9
9379 TATTTGTTTC
9389 TTTTATTAT
1 TTTTATTAT
9398 TTTTATTAT
1 TTTTATTAT
9407 TTTTATTAT
1 TTTTATTAT
*
9416 GTTCTT-TAAT
1 -TT-TTATTAT
9426 TTTT-TT-T
1 TTTTATTAT
9433 GTTTTATTAT
1 -TTTTATTAT
*
9443 TATTATTAT
1 TTTTATTAT
*
9452 TCTTATTTAT
1 TTTTA-TTAT
9462 TATTTA-T-T
1 T-TTTATTAT
*
9470 TTATATTAT
1 TTTTATTAT
9479 TTTT
1 TTTT
9483 CTTCTTACTA
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
7 4 0.06
8 10 0.14
9 39 0.57
10 11 0.16
11 5 0.07
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTATTAT
Found at i:9477 original size:36 final size:36
Alignment explanation
Indices: 9394--9548 Score: 88
Period size: 36 Copynumber: 4.2 Consensus size: 36
9384 GTTTCTTTTA
* * *
9394 TTATTTT-TATTATTTTTATTA-TGTTCTTTAATT-T
1 TTATTTTATATTATTATTATTATTCTTATTT-ATTAT
* *
9428 TTTTTGTTTTATTATTATTATTATTCTTATTTATTAT
1 TTATT-TTATATTATTATTATTATTCTTATTTATTAT
* * * *
9465 TTATTTTATATTATTTTTCTTCTTACTATATTT-TTCT
1 TTATTTTATATTATTATTATTATT-CT-TATTTATTAT
*
9502 AATATTTTATATATATATATTATTTTATTTCTTA-TTATTAT
1 -TTATTTTATAT-TAT-TATTA--TTA-TTCTTATTTATTAT
9543 TT-TTTT
1 TTATTTT
9549 CTAATATTTT
Statistics
Matches: 92, Mismatches: 16, Indels: 21
0.71 0.12 0.16
Matches are distributed among these distances:
34 4 0.04
35 2 0.02
36 31 0.34
37 16 0.17
38 15 0.16
39 7 0.08
40 6 0.07
41 5 0.05
42 4 0.04
43 2 0.02
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (36 bp):
TTATTTTATATTATTATTATTATTCTTATTTATTAT
Found at i:9579 original size:2 final size:2
Alignment explanation
Indices: 9572--9600 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9562 TATACGTTAT
9572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9601 TACTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9628 original size:13 final size:13
Alignment explanation
Indices: 9610--9694 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 13
9600 TTACTTTATT
*
9610 TCTTTTTTGTTTA
1 TCTTTTTTATTTA
*
9623 TCTTTTTTTCGTTTTA
1 TC-TTTTTT--ATTTA
9639 T-TTTTTTATTT-
1 TCTTTTTTATTTA
* *
9650 TATTCTTTATTTA
1 TCTTTTTTATTTA
*
9663 TC-TCTTT-TTTA
1 TCTTTTTTATTTA
*
9674 TTTTTTTTATTTA
1 TCTTTTTTATTTA
9687 T-TTTTTTA
1 TCTTTTTTA
9695 ATCATTCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
11 6 0.10
12 28 0.47
13 8 0.14
14 12 0.20
16 5 0.08
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (13 bp):
TCTTTTTTATTTA
Found at i:9631 original size:14 final size:15
Alignment explanation
Indices: 9604--9645 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
9594 TATATATTAC
*
9604 TTTATTTCTTTTTTG-
1 TTTATTT-TTTTTCGT
9619 TTTATCTTTTTTTCGT
1 TTTAT-TTTTTTTCGT
9635 TTTATTTTTTT
1 TTTATTTTTTT
9646 ATTTTATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTATTTTTTTTCGT
Found at i:9658 original size:20 final size:19
Alignment explanation
Indices: 9634--9690 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
9624 CTTTTTTTCG
9634 TTTTATTTTTTTATTTTAT
1 TTTTATTTTTTTATTTTAT
9653 TCTTTATTTATCTCTT-TTTTAT
1 T-TTTATTT-T-T-TTATTTTAT
*
9675 TTTT-TTTATTTATTTT
1 TTTTATTTTTTTATTTT
9691 TTTAATCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 1 0.03
20 10 0.31
21 4 0.12
22 8 0.25
23 2 0.06
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTTTATTTTAT
Found at i:9662 original size:24 final size:23
Alignment explanation
Indices: 9635--9728 Score: 88
Period size: 24 Copynumber: 4.1 Consensus size: 23
9625 TTTTTTTCGT
9635 TTTATTTTTTTATTTTATTCTTTA
1 TTTATTTTTTT-TTTTATTCTTTA
* *
9659 TTTA-TCTCTTTTTTATT-TTT-
1 TTTATTTTTTTTTTTATTCTTTA
* * *
9679 TTTATTTATTTTTTTAATCATTCA
1 TTTATTTTTTTTTTTATTC-TTTA
9703 TTTATTTTTTTTCTTTA-TCTTTA
1 TTTATTTTTTTT-TTTATTCTTTA
9726 TTT
1 TTT
9729 TATCTTGTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.07
21 12 0.21
22 7 0.12
23 12 0.21
24 17 0.30
25 4 0.07
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTTTTTTTTTATTCTTTA
Found at i:9673 original size:11 final size:10
Alignment explanation
Indices: 9647--9684 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
9637 TATTTTTTTA
9647 TTTTATTCTT
1 TTTTATTCTT
9657 TATTTATCTCTT
1 T-TTTAT-TCTT
9669 TTTTATT-TT
1 TTTTATTCTT
9678 TTTTATT
1 TTTTATT
9685 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.35
10 2 0.08
11 10 0.38
12 5 0.19
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATTCTT
Found at i:9691 original size:20 final size:22
Alignment explanation
Indices: 9647--9888 Score: 62
Period size: 23 Copynumber: 10.8 Consensus size: 22
9637 TATTTTTTTA
*
9647 TTTTATTCTTTATTTATCTCTT
1 TTTTATTCTTTATTTATCTATT
*
9669 TTTTATT-TTT-TTTATTTATTT
1 TTTTATTCTTTATTTATCTA-TT
* * *
9690 TTTTAATCATTCATTTAT-TTTT
1 TTTTATTC-TTTATTTATCTATT
* *
9712 TTTCTTTATCTTTATTTTATCTTGTT
1 TTT-TAT-TCTTTA-TTTATC-TATT
* *
9738 TATTTA-TGTATATTTATCT-TT
1 T-TTTATTCTTTATTTATCTATT
*
9759 ATTTTATTTCTTTCATTT-TCTCTAT
1 -TTTTA-TTCTTT-ATTTATCTAT-T
* *
9784 CTTTA-T-TTTAATTATGCTATT
1 TTTTATTCTTTATTTAT-CTATT
9805 TACATTT-TATCTTTACTTTA--TA-T
1 T---TTTAT-TCTTTA-TTTATCTATT
*
9828 TTTTATTGTTTATTTCATCTA-T
1 TTTTATTCTTTATTT-ATCTATT
* * *
9850 TTTTACTTCTTTATTTTTTTCTT
1 TTTTA-TTCTTTATTTATCTATT
*
9873 CTTTATT-TTTATTTAT
1 TTTTATTCTTTATTTAT
9889 TTTCATCACC
Statistics
Matches: 163, Mismatches: 26, Indels: 63
0.65 0.10 0.25
Matches are distributed among these distances:
19 3 0.02
20 18 0.11
21 31 0.19
22 30 0.18
23 35 0.21
24 30 0.18
25 2 0.01
26 9 0.06
27 5 0.03
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTCTTTATTTATCTATT
Found at i:9730 original size:24 final size:23
Alignment explanation
Indices: 9634--9763 Score: 81
Period size: 24 Copynumber: 5.4 Consensus size: 23
9624 CTTTTTTTCG
9634 TTTTATTTTTTTATTTTATTCTTTA
1 TTTTATTTTTTT-TTTTA-TCTTTA
* *
9659 -TTTA-TCTCTTTTTTAT-TTT-
1 TTTTATTTTTTTTTTTATCTTTA
* *
9678 TTTTATTTATTTTTTTAATCATTCA
1 TTTTATTT-TTTTTTTTATC-TTTA
9703 -TTTATTTTTTTTCTTTATCTTTA
1 TTTTATTTTTTTT-TTTATCTTTA
*
9726 TTTTATCTTGTTTATTTATGTATATTTA
1 TTTTAT-TT-TTT-TTT-T-TATCTTTA
9754 TCTTTATTTT
1 T-TTTATTTT
9764 ATTTCTTTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
20 7 0.09
21 2 0.02
22 13 0.16
23 12 0.15
24 23 0.28
25 2 0.02
26 4 0.05
27 4 0.05
28 10 0.12
29 5 0.06
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTTTTTTTATCTTTA
Found at i:9854 original size:15 final size:14
Alignment explanation
Indices: 9829--9886 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
9819 ACTTTATATT
9829 TTTATTGTTTATTTC
1 TTTATT-TTTATTTC
* *
9844 ATCTATTTTTACTTC
1 -TTTATTTTTATTTC
*
9859 TTTATTTTTTTCTTC
1 TTTATTTTTAT-TTC
9874 TTTATTTTTATTT
1 TTTATTTTTATTT
9887 ATTTTCATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 10 0.29
15 20 0.57
16 5 0.14
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTATTTTTATTTC
Found at i:11916 original size:23 final size:23
Alignment explanation
Indices: 11898--11957 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
11888 GTTTTAGGTT
*
11898 CGGGTTTAGGCTTGGTTTAGATC
1 CGGGTTCAGGCTTGGTTTAGATC
*
11921 CGGGTTCAGTCTTGGTTTAGATC
1 CGGGTTCAGGCTTGGTTTAGATC
*
11944 CGGGTTCGGGCTTG
1 CGGGTTCAGGCTTG
11958 TAATTGTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.10, C:0.17, G:0.37, T:0.37
Consensus pattern (23 bp):
CGGGTTCAGGCTTGGTTTAGATC
Found at i:14708 original size:3 final size:3
Alignment explanation
Indices: 14694--14803 Score: 91
Period size: 3 Copynumber: 35.3 Consensus size: 3
14684 TTTTGTCGGA
* *
14694 ATT ATT AGTT ATT ATTT ATT ATT ATT ATTT ACT ATT AATA ATT ATTT
1 ATT ATT A-TT ATT A-TT ATT ATT ATT A-TT ATT ATT -ATT ATT A-TT
* *
14741 ATT A-T ATA ATT ATT ATT ATT ATT -TT A-T ATT ATT AGTT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
*
14784 ACTA ATT ATT ATT ATT ATT A
1 A-TT ATT ATT ATT ATT ATT A
14804 GAAGTCCAAC
Statistics
Matches: 87, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
2 6 0.07
3 62 0.71
4 19 0.22
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:14720 original size:13 final size:13
Alignment explanation
Indices: 14695--14802 Score: 101
Period size: 13 Copynumber: 8.1 Consensus size: 13
14685 TTTGTCGGAA
14695 TTATTAGTTATTAT
1 TTATTA-TTATTAT
14709 TTATTATTATTAT
1 TTATTATTATTAT
* * *
14722 TTACTATTAATAA
1 TTATTATTATTAT
*
14735 TTATTTATTATATAA
1 TTA-TTATTAT-TAT
14750 TTATTATTATTAT
1 TTATTATTATTAT
*
14763 TT-TATATTATTAG
1 TTAT-TATTATTAT
* * *
14776 TTACTATTACTAA
1 TTATTATTATTAT
14789 TTATTATTATTAT
1 TTATTATTATTAT
14802 T
1 T
14803 AGAAGTCCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
12 1 0.01
13 52 0.68
14 18 0.23
15 6 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:15353 original size:43 final size:44
Alignment explanation
Indices: 15260--15354 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 44
15250 TCCGGATTTG
* **
15260 ATAGTTATATATTAAAAAATAATTAATTAGTTTGTTTGTTAGTCG
1 ATAGTTATATA-TAAAAAATAATTAATTAGTTTGTTAGTTAGTAA
* *
15305 TTAGTTATATA-AAAAAATATTTAATTAGTTTG-TAGTTAGTTAA
1 ATAGTTATATATAAAAAATAATTAATTAGTTTGTTAGTTAG-TAA
15348 ATAGTTA
1 ATAGTTA
15355 AGTTATATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
42 6 0.14
43 27 0.63
45 10 0.23
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (44 bp):
ATAGTTATATATAAAAAATAATTAATTAGTTTGTTAGTTAGTAA
Found at i:16014 original size:23 final size:23
Alignment explanation
Indices: 15937--16014 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 23
15927 AAGATCTAAT
15937 AATTTAAGAACAAAAATTACATA
1 AATTTAAGAACAAAAATTACATA
* * *
15960 AATTCAACTTCAATATAAAGATCTA-AT-
1 AATTTAA---GAACA-AAA-AT-TACATA
15987 AATTTAAGAACAAAAATTACATA
1 AATTTAAGAACAAAAATTACATA
16010 AATTT
1 AATTT
16015 CCTTGCAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 16
0.65 0.10 0.25
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
23 14 0.34
24 3 0.07
26 3 0.07
27 9 0.22
28 4 0.10
29 2 0.05
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (23 bp):
AATTTAAGAACAAAAATTACATA
Found at i:17221 original size:16 final size:16
Alignment explanation
Indices: 17200--17281 Score: 110
Period size: 16 Copynumber: 5.1 Consensus size: 16
17190 TCGGGATCAC
17200 ATGGCGACCTCCATTT
1 ATGGCGACCTCCATTT
17216 ATGGCGACCTCCATTT
1 ATGGCGACCTCCATTT
*
17232 ATGGCGACCTCAATTT
1 ATGGCGACCTCCATTT
* * ***
17248 ATGGTGACCTTCACGC
1 ATGGCGACCTCCATTT
17264 ATGGCGACCTCCATTT
1 ATGGCGACCTCCATTT
17280 AT
1 AT
17282 TCCGTGGGTG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (16 bp):
ATGGCGACCTCCATTT
Found at i:17642 original size:7 final size:7
Alignment explanation
Indices: 17630--17745 Score: 62
Period size: 7 Copynumber: 16.1 Consensus size: 7
17620 TTTGTCGGAA
*
17630 TTATTAG
1 TTATTAT
17637 TTATTAT
1 TTATTAT
17644 TTATTA-
1 TTATTAT
17650 TTATTAT
1 TTATTAT
17657 TTATTAT
1 TTATTAT
17664 TAATAATTAT
1 T--T-ATTAT
17674 TTATTACT
1 TTATTA-T
* *
17682 ATCATTAA
1 -TTATTAT
17690 TTATTA-
1 TTATTAT
*
17696 ATATTA-
1 TTATTAT
17702 TTATT-T
1 TTATTAT
17708 TATATTAT
1 T-TATTAT
*
17716 TGATTACT
1 TTATTA-T
* *
17724 ATTACTAA
1 -TTATTAT
17732 TTATTA-
1 TTATTAT
17738 TTATTAT
1 TTATTAT
17745 T
1 T
17746 AGAAGTCCAA
Statistics
Matches: 86, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
6 22 0.26
7 43 0.50
8 5 0.06
9 10 0.12
10 6 0.07
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (7 bp):
TTATTAT
Found at i:17643 original size:3 final size:3
Alignment explanation
Indices: 17629--17746 Score: 96
Period size: 3 Copynumber: 37.3 Consensus size: 3
17619 TTTTGTCGGA
*
17629 ATT ATT AGTT ATT ATTT ATT ATT ATT ATTT ATT ATT AATA ATT ATTT
1 ATT ATT A-TT ATT A-TT ATT ATT ATT A-TT ATT ATT -ATT ATT A-TT
* * *
17676 ATT ACT ATC ATT AATT ATT AAT ATT ATT ATT -TT A-T ATT ATT GATT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* *
17721 ACT ATT ACTA ATT ATT ATT ATT ATT A
1 ATT ATT A-TT ATT ATT ATT ATT ATT A
17747 GAAGTCCAAC
Statistics
Matches: 93, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
2 4 0.04
3 67 0.72
4 22 0.24
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:17654 original size:20 final size:19
Alignment explanation
Indices: 17629--17746 Score: 100
Period size: 20 Copynumber: 6.2 Consensus size: 19
17619 TTTTGTCGGA
*
17629 ATTATTAGTTATTATTTATT
1 ATTATTATTTATTA-TTATT
17649 ATTATTATTTATTATTA--
1 ATTATTATTTATTATTATT
* * *
17666 ATAATTATTTATTACTATC
1 ATTATTATTTATTATTATT
*
17685 ATTAATTA-TTAATATTATT
1 ATT-ATTATTTATTATTATT
*
17704 ATT-TTATATTATTGATTACT
1 ATTATTAT-TTATT-ATTATT
* *
17724 ATTACTAATTATTATTATT
1 ATTATTATTTATTATTATT
17743 ATTA
1 ATTA
17747 GAAGTCCAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
17 18 0.23
19 29 0.37
20 30 0.38
21 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTATTATTTATTATTATT
Found at i:17655 original size:13 final size:13
Alignment explanation
Indices: 17630--17745 Score: 82
Period size: 13 Copynumber: 9.1 Consensus size: 13
17620 TTTGTCGGAA
17630 TTATTAGTTATTAT
1 TTATTA-TTATTAT
17644 TTATTATTATTAT
1 TTATTATTATTAT
* *
17657 TTATTATTAATAA
1 TTATTATTATTAT
17670 TTA-T-TTATTA-
1 TTATTATTATTAT
* *
17680 CTATCATTAATTA-
1 TTATTATT-ATTAT
*
17693 TTAATATTATTAT
1 TTATTATTATTAT
17706 TT-TATATTATTGA-
1 TTAT-TATTATT-AT
* * *
17719 TTACTATTACTAA
1 TTATTATTATTAT
17732 TTATTATTATTAT
1 TTATTATTATTAT
17745 T
1 T
17746 AGAAGTCCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
10 2 0.03
11 5 0.06
12 8 0.10
13 58 0.73
14 7 0.09
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:17715 original size:42 final size:45
Alignment explanation
Indices: 17639--17746 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 45
17629 ATTATTAGTT
* *
17639 ATTATTTATTATTATTATTTATTATTAATAATTATTTATTACTATC
1 ATTAATTATTATTATTA-TTATTATTAATAATTATTGATTACTATC
* *
17685 ATTAATTATTAATATTATTATT-TT-AT-ATTATTGATTACTATT
1 ATTAATTATTATTATTATTATTATTAATAATTATTGATTACTATC
*
17727 ACTAATTATTATTATTATTA
1 ATTAATTATTATTATTATTA
17747 GAAGTCCAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 32 0.57
43 2 0.04
44 2 0.04
45 5 0.09
46 15 0.27
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (45 bp):
ATTAATTATTATTATTATTATTATTAATAATTATTGATTACTATC
Found at i:19041 original size:43 final size:44
Alignment explanation
Indices: 18954--19042 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 44
18944 TTGATAGTTA
* ***
18954 TATATTAAAAAAATAATTAATTAGTTTGTTTGTTAGTCGTTAGT
1 TATATTAAAAAAATAATTAATTAGTTTGTTAGTTAGTAAATAGT
*
18998 TATA-TAAAAAAATATTTAATTAGTTTG-TAGTTAGTTAAATAGT
1 TATATTAAAAAAATAATTAATTAGTTTGTTAGTTAG-TAAATAGT
19041 TA
1 TA
19043 AGTTATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 6 0.15
43 29 0.74
44 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.46
Consensus pattern (44 bp):
TATATTAAAAAAATAATTAATTAGTTTGTTAGTTAGTAAATAGT
Found at i:21649 original size:29 final size:29
Alignment explanation
Indices: 21603--21689 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
21593 AGTGTTGGCC
21603 GTAGGTCGCCATGCCTTCCGGGTGACCTT
1 GTAGGTCGCCATGCCTTCCGGGTGACCTT
*
21632 GTAGGTCGCCATGTCTTCCGGGTGACCTT
1 GTAGGTCGCCATGCCTTCCGGGTGACCTT
* *
21661 GTAGGTCACCATGCCTTCCGGGCGACCTT
1 GTAGGTCGCCATGCCTTCCGGGTGACCTT
21690 ATCTCTGCCT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.11, C:0.31, G:0.30, T:0.28
Consensus pattern (29 bp):
GTAGGTCGCCATGCCTTCCGGGTGACCTT
Found at i:21811 original size:26 final size:26
Alignment explanation
Indices: 21723--21798 Score: 125
Period size: 27 Copynumber: 2.9 Consensus size: 26
21713 ACGTCTCCAA
*
21723 CAATCATGCACATCTCGCCATGCCTT
1 CAATCATGCACGTCTCGCCATGCCTT
*
21749 CAATCATGCACCGTCTCACCATGCCTT
1 CAATCATGCA-CGTCTCGCCATGCCTT
21776 CAATCATGCACGTCTCGCCATGC
1 CAATCATGCACGTCTCGCCATGC
21799 TTTCCCGCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 22 0.48
27 24 0.52
ACGTcount: A:0.22, C:0.39, G:0.13, T:0.25
Consensus pattern (26 bp):
CAATCATGCACGTCTCGCCATGCCTT
Found at i:22096 original size:26 final size:26
Alignment explanation
Indices: 22056--22113 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
22046 ACATAAAAGA
*
22056 AAGAAAGGGAGAAGATATTGCAGCCG
1 AAGAAAGGGAGAAGAGATTGCAGCCG
* *
22082 AAGAAAGGGATAAGAGATTGCTGCCG
1 AAGAAAGGGAGAAGAGATTGCAGCCG
22108 -AGAAAG
1 AAGAAAG
22114 AAAGAAATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.43, C:0.10, G:0.34, T:0.12
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAGATTGCAGCCG
Found at i:22298 original size:21 final size:22
Alignment explanation
Indices: 22259--22299 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
22249 GTTAATTAGT
*
22259 TTGTTAGTTTAGGGTTATATGA
1 TTGTTAGTTTAGAGTTATATGA
22281 TTGTTAGTTTA-AGTTATAT
1 TTGTTAGTTTAGAGTTATAT
22300 TATACAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (22 bp):
TTGTTAGTTTAGAGTTATATGA
Found at i:22389 original size:39 final size:40
Alignment explanation
Indices: 22310--22434 Score: 101
Period size: 39 Copynumber: 3.1 Consensus size: 40
22300 TATACAGAAA
* * * *
22310 TAAAAAATTATTTAATTAGTATG-TTTGATAGTTATATAGT
1 TAAAAAA-TAATTAATTAGTTTGTTTTGTTAGTCATATAGT
*
22350 TAAAAAATAATTAATTAGTTTGTTTTGTTAGTCGT-TAGT
1 TAAAAAATAATTAATTAGTTTGTTTTGTTAGTCATATAGT
* * * * * *
22389 TATATAAAAAAATTATTTAATTAGTTTATGTTAGTTAAATAGT
1 TA-A-AAAATAATTAATTAGTTTGTTT-TGTTAGTCATATAGT
22432 TAA
1 TAA
22435 GTTATATTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
39 19 0.28
40 17 0.25
41 18 0.26
42 8 0.12
43 6 0.09
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (40 bp):
TAAAAAATAATTAATTAGTTTGTTTTGTTAGTCATATAGT
Found at i:22432 original size:43 final size:40
Alignment explanation
Indices: 22311--22434 Score: 106
Period size: 43 Copynumber: 3.0 Consensus size: 40
22301 ATACAGAAAT
* *
22311 AAAAAATTATTTAATTAGTATGTTTGATAGTTATATAGTTAAA
1 AAAAAATTATTTAATTAG--T-TTTGTTAGTTAAATAGTTAAA
* * * * ***
22354 AAATAATTAATTAGTTTGTTTTGTTAG-TCGTTAGTTATATA
1 AAAAAATTATTTAATTAGTTTTGTTAGTTAAATAGTTA-A-A
22395 AAAAAATTATTTAATTAGTTTATGTTAGTTAAATAGTTAA
1 AAAAAATTATTTAATTAGTTT-TGTTAGTTAAATAGTTAA
22435 GTTATATTTG
Statistics
Matches: 62, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
39 7 0.11
40 8 0.13
41 19 0.31
42 7 0.11
43 21 0.34
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (40 bp):
AAAAAATTATTTAATTAGTTTTGTTAGTTAAATAGTTAAA
Found at i:22640 original size:11 final size:12
Alignment explanation
Indices: 22626--22735 Score: 54
Period size: 11 Copynumber: 9.2 Consensus size: 12
22616 TTAGTTCATT
22626 ATTATC-AAATC
1 ATTATCTAAATC
22637 ATTA-CTAAATC
1 ATTATCTAAATC
* *
22648 ATTAT-TATCATT
1 ATTATCTA-AATC
22660 ATTAT-TAAATC
1 ATTATCTAAATC
* *
22671 AATAT-TATAATG
1 ATTATCTA-AATC
22683 ATTATTACTAAATC
1 ATTA-T-CTAAATC
*
22697 ATTAT-TATAATG
1 ATTATCTA-AATC
*
22709 ATTATTATCAAATC
1 ATTA-TCT-AAATC
22723 ATTA-CTAAATC
1 ATTATCTAAATC
22734 AT
1 AT
22736 CAAATCATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
10 1 0.01
11 32 0.42
12 23 0.30
13 3 0.04
14 15 0.19
15 3 0.04
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (12 bp):
ATTATCTAAATC
Found at i:22660 original size:34 final size:35
Alignment explanation
Indices: 22621--22689 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
22611 GTTTATTAGT
*
22621 TCATTATTATCAAATCATTACTA-AATCATTATTA
1 TCATTATTATCAAATCAATACTATAATCATTATTA
* * *
22655 TCATTATTATTAAATCAATATTATAATGATTATTA
1 TCATTATTATCAAATCAATACTATAATCATTATTA
22690 CTAAATCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 20 0.67
35 10 0.33
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.46
Consensus pattern (35 bp):
TCATTATTATCAAATCAATACTATAATCATTATTA
Found at i:22668 original size:23 final size:23
Alignment explanation
Indices: 22621--22704 Score: 87
Period size: 26 Copynumber: 3.4 Consensus size: 23
22611 GTTTATTAGT
*
22621 TCATTATTATCAAATCATTACTAAA
1 TCATTATTATC--ATTATTACTAAA
*
22646 TCATTATTATCATTATTATTAAA
1 TCATTATTATCATTATTACTAAA
* *
22669 TCAATATTATAATGATTATTACTAAA
1 TC---ATTATTATCATTATTACTAAA
22695 TCATTATTAT
1 TCATTATTAT
22705 AATGATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
23 19 0.38
25 11 0.22
26 20 0.40
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.46
Consensus pattern (23 bp):
TCATTATTATCATTATTACTAAA
Found at i:22677 original size:26 final size:26
Alignment explanation
Indices: 22648--22723 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
22638 TTACTAAATC
* *
22648 ATTATTATCATTATTATTAAATCAAT
1 ATTATAATGATTATTATTAAATCAAT
* *
22674 ATTATAATGATTATTACTAAATCATT
1 ATTATAATGATTATTATTAAATCAAT
*
22700 ATTATAATGATTATTATCAAATCA
1 ATTATAATGATTATTATTAAATCA
22724 TTACTAAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTATAATGATTATTATTAAATCAAT
Found at i:22701 original size:37 final size:37
Alignment explanation
Indices: 22654--22735 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 37
22644 AATCATTATT
*
22654 ATCATTATTATTAAATCAATATTAT-AATGATTATTACTAA
1 ATCATTATTA-T-AATCAATATTATCAA--ATCATTACTAA
* *
22694 ATCATTATTATAATGATTATTATCAAATCATTACTAA
1 ATCATTATTATAATCAATATTATCAAATCATTACTAA
22731 ATCAT
1 ATCAT
22736 CAAATCATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 15 0.39
38 10 0.26
39 3 0.08
40 10 0.26
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (37 bp):
ATCATTATTATAATCAATATTATCAAATCATTACTAA
Found at i:22712 original size:23 final size:23
Alignment explanation
Indices: 22621--22712 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 23
22611 GTTTATTAGT
*
22621 TCATTATTATCAAATCATTACTAAA
1 TCATTATTAT--AATGATTACTAAA
* * *
22646 TCATTATTATCATTATTATTAAA
1 TCATTATTATAATGATTACTAAA
*
22669 TCAATATTATAATGATTATTACTAAA
1 TCATTATTATAATG---ATTACTAAA
22695 TCATTATTATAATGATTA
1 TCATTATTATAATGATTA
22713 TTATCAAATC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
23 25 0.45
25 10 0.18
26 21 0.38
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (23 bp):
TCATTATTATAATGATTACTAAA
Found at i:22999 original size:49 final size:49
Alignment explanation
Indices: 22936--23048 Score: 199
Period size: 49 Copynumber: 2.3 Consensus size: 49
22926 ATTACTAATA
22936 ATTACTAAATCATTACTATCAAATCATTAAATATTAAAAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAAAAATAATTTCATT
* *
22986 ATTACTAATCATTACTTTCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAAAAATAATTTCATT
23035 ATTACTAATCATTA
1 ATTACTAATCATTA
23049 AATAATAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
49 55 0.90
50 6 0.10
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAAAAATAATTTCATT
Found at i:23031 original size:27 final size:27
Alignment explanation
Indices: 22954--23032 Score: 69
Period size: 25 Copynumber: 3.1 Consensus size: 27
22944 ATCATTACTA
*
22954 TCAAATCATTAAATATTAAAAATAATT
1 TCAAATCATTAAATATTAATAATAATT
* * * * *
22981 TC--ATTATT-ACTAATCAT--TACTT
1 TCAAATCATTAAATATTAATAATAATT
23003 TCAAATCATTAAATATTAATAATAATT
1 TCAAATCATTAAATATTAATAATAATT
23030 TCA
1 TCA
23033 TTATTACTAA
Statistics
Matches: 36, Mismatches: 11, Indels: 10
0.63 0.19 0.18
Matches are distributed among these distances:
22 6 0.17
24 10 0.28
25 11 0.31
27 9 0.25
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (27 bp):
TCAAATCATTAAATATTAATAATAATT
Found at i:23043 original size:18 final size:18
Alignment explanation
Indices: 23016--23078 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
23006 AATCATTAAA
23016 TATTAATAATAATTTCAT
1 TATTAATAATAATTTCAT
* * * *
23034 TATTACTAATCA-TTAAA
1 TATTAATAATAATTTCAT
*
23051 TAATAATAATAATTTCAT
1 TATTAATAATAATTTCAT
*
23069 TATTACTAAT
1 TATTAATAAT
23079 CATTACTAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTAATAATAATTTCAT
Found at i:23060 original size:32 final size:34
Alignment explanation
Indices: 23006--23092 Score: 129
Period size: 35 Copynumber: 2.5 Consensus size: 34
22996 ATTACTTTCA
*
23006 AATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATT-AATAATAATAATAATTTCATTATTACT
23041 AATCATTAAATAATAATAATAATTTCATTATTACT
1 AATCATT-AATAATAATAATAATTTCATTATTACT
*
23076 AATCATTACTAAATAAT
1 AATCATTAAT-AATAAT
23093 TATTATAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 2 0.04
35 47 0.96
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (34 bp):
AATCATTAATAATAATAATAATTTCATTATTACT
Found at i:23103 original size:38 final size:35
Alignment explanation
Indices: 23006--23083 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
22996 ATTACTTTCA
*
23006 AATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTAAATAATAATAATAATTTCATTATTACT
23041 AATCATTAAATAATAATAATAATTTCATTATTACT
1 AATCATTAAATAATAATAATAATTTCATTATTACT
23076 AATCATTA
1 AATCATTA
23084 CTAAATAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (35 bp):
AATCATTAAATAATAATAATAATTTCATTATTACT
Found at i:23158 original size:21 final size:21
Alignment explanation
Indices: 23134--23194 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 21
23124 AATCATGATT
23134 ATCAAATCATTACTAAATCAA
1 ATCAAATCATTACTAAATCAA
23155 ATC--AT-A-T-CTAAATCAA
1 ATCAAATCATTACTAAATCAA
*
23171 ATCATATCATTA-T-AAT-AA
1 ATCAAATCATTACTAAATCAA
23189 ATCAAA
1 ATCAAA
23195 CAAGTGTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
16 12 0.35
17 1 0.03
18 10 0.29
19 6 0.18
20 2 0.06
21 3 0.09
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATCAAATCATTACTAAATCAA
Found at i:23176 original size:16 final size:16
Alignment explanation
Indices: 23134--23178 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
23124 AATCATGATT
23134 ATCAAATCAT-TACTAA
1 ATCAAATCATAT-CTAA
23150 ATCAAATCATATCTAA
1 ATCAAATCATATCTAA
23166 ATCAAATCATATC
1 ATCAAATCATATC
23179 ATTATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
ATCAAATCATATCTAA
Found at i:26770 original size:28 final size:28
Alignment explanation
Indices: 26739--26792 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
26729 ACAATCTAAT
26739 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
26767 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
26793 ATTTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:26799 original size:28 final size:28
Alignment explanation
Indices: 26735--26799 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
26725 TTATACAATC
26735 TAATATATAACTTAAACTAACAAACTAA
1 TAATATATAACTTAAACTAACAAACTAA
26763 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
26791 TAATTTATA
1 TAATATATA
26800 CTAACAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:26802 original size:21 final size:21
Alignment explanation
Indices: 26769--26817 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
26759 CTAATATAAT
26769 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
26790 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
26811 ATTAACT
1 A-TAACT
26818 AAATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:26954 original size:5 final size:5
Alignment explanation
Indices: 26944--26977 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
26934 TTCTTCTTCT
26944 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
26978 TCTCGCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCC
Found at i:27611 original size:30 final size:30
Alignment explanation
Indices: 27577--27646 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
27567 CTTGGGAGTG
27577 CATTATCTCGTGAAATAATTTCTTCGAGAA
1 CATTATCTCGTGAAATAATTTCTTCGAGAA
27607 CATTATCTCGTGAAATAATTTCTTCGAGAA
1 CATTATCTCGTGAAATAATTTCTTCGAGAA
27637 CATTATCTCG
1 CATTATCTCG
27647 AGAGTTTTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (30 bp):
CATTATCTCGTGAAATAATTTCTTCGAGAA
Found at i:29043 original size:20 final size:20
Alignment explanation
Indices: 29020--29074 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
29010 AAATTCGCAA
*
29020 TGCGATTTTGAAAAATGTGT
1 TGCGATATTGAAAAATGTGT
29040 TGCGATAGTT--AAAATGTGT
1 TGCGATA-TTGAAAAATGTGT
*
29059 TGCGATAGTGAAAAAT
1 TGCGATATTGAAAAAT
29075 CCAAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 11 0.37
21 2 0.07
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
TGCGATATTGAAAAATGTGT
Found at i:29055 original size:19 final size:19
Alignment explanation
Indices: 29031--29072 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
29021 GCGATTTTGA
*
29031 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
29050 AAAATGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
29069 AAAA
1 AAAA
29073 ATCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:29291 original size:14 final size:14
Alignment explanation
Indices: 29272--29325 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
29262 TTCGTGAACA
29272 TTCGGTTATGTTCG
1 TTCGGTTATGTTCG
29286 TTCGGTTATGTTCG
1 TTCGGTTATGTTCG
*
29300 -T---TTATGTTTG
1 TTCGGTTATGTTCG
29310 TTCGGTTATGTTCG
1 TTCGGTTATGTTCG
29324 TT
1 TT
29326 TATGTTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.07, C:0.11, G:0.26, T:0.56
Consensus pattern (14 bp):
TTCGGTTATGTTCG
Found at i:29345 original size:24 final size:24
Alignment explanation
Indices: 29272--29332 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
29262 TTCGTGAACA
*
29272 TTCGGTTATGTTCGTTCGGTTATG
1 TTCGTTTATGTTCGTTCGGTTATG
*
29296 TTCGTTTATGTTTGTTCGGTTATG
1 TTCGTTTATGTTCGTTCGGTTATG
29320 TTCGTTTATGTTC
1 TTCGTTTATGTTC
29333 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.08, C:0.11, G:0.25, T:0.56
Consensus pattern (24 bp):
TTCGTTTATGTTCGTTCGGTTATG
Found at i:30452 original size:14 final size:16
Alignment explanation
Indices: 30417--30457 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
30407 GTCTCCAACG
*
30417 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTTC
30433 TTTATGTT-GTG-TTC
1 TTTATGTTCGTGTTTC
30447 TTTATGTTCGT
1 TTTATGTTCGT
30458 TTATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.43
15 5 0.22
16 8 0.35
ACGTcount: A:0.07, C:0.07, G:0.22, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTTC
Found at i:31109 original size:41 final size:39
Alignment explanation
Indices: 31036--31175 Score: 147
Period size: 41 Copynumber: 3.5 Consensus size: 39
31026 CGAATTTGGA
** *
31036 AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTAC
1 AAATCGCATTGCGATTTTCAAAATCGCGTTGCGATTTAC
* *
31075 ATATTCGCATTGCGATTTTCTAAAATCGCGTTGCGATAGT-C
1 A-AATCGCATTGCGATTTTC-AAAATCGCGTTGCGAT-TTAC
* *
31116 AAAATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTTAG
1 -AAATCGCATTGCGATTTT-CAAAATCGCGTTGCGA-TTTAC
*
31158 AGATCGCATTGCGATTTT
1 AAATCGCATTGCGATTTT
31176 GTTGGTCATT
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
39 1 0.01
40 15 0.18
41 64 0.76
42 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (39 bp):
AAATCGCATTGCGATTTTCAAAATCGCGTTGCGATTTAC
Found at i:31113 original size:61 final size:62
Alignment explanation
Indices: 31035--31172 Score: 183
Period size: 61 Copynumber: 2.3 Consensus size: 62
31025 ACGAATTTGG
* * *
31035 AAAATCGCATTGCGATAGTCAGAATCGCGTTGCGA-TTTACATATTCGCATTGCGATTTTCT
1 AAAATCGCATTGCGATAGTCAAAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTTCT
* * *
31096 AAAATCGCGTTGCGATAGTCAAAATCGCATTGCGATTTTCCAAATTCGCGTTGCGA-TTT-T
1 AAAATCGCATTGCGATAGTCAAAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTTCT
*
31156 AGAGATCGCATTGCGAT
1 A-AAATCGCATTGCGAT
31173 TTTGTTGGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 2 0.03
61 48 0.72
62 17 0.25
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (62 bp):
AAAATCGCATTGCGATAGTCAAAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTTCT
Found at i:31140 original size:20 final size:20
Alignment explanation
Indices: 31036--31175 Score: 104
Period size: 20 Copynumber: 6.9 Consensus size: 20
31026 CGAATTTGGA
**
31036 AAATCGCATTGCGATAGT-C
1 AAATCGCATTGCGATTTTCC
* *
31055 AGAATCGCGTTGCGA-TTTAC
1 A-AATCGCATTGCGATTTTCC
* *
31075 ATATTCGCATTGCGATTTTCTA
1 A-AATCGCATTGCGATTTTC-C
* ** *
31097 AAATCGCGTTGCGATAGTCA
1 AAATCGCATTGCGATTTTCC
31117 AAATCGCATTGCGATTTTCC
1 AAATCGCATTGCGATTTTCC
* **
31137 AAATTCGCGTTGCGATTTTAG
1 AAA-TCGCATTGCGATTTTCC
*
31158 AGATCGCATTGCGATTTT
1 AAATCGCATTGCGATTTT
31176 GTTGGTCATT
Statistics
Matches: 95, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.02
20 59 0.62
21 33 0.35
22 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
AAATCGCATTGCGATTTTCC
Found at i:32578 original size:22 final size:21
Alignment explanation
Indices: 32553--32593 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
32543 TAATTTAAAT
32553 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
32575 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
32594 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:35446 original size:165 final size:165
Alignment explanation
Indices: 35109--35456 Score: 514
Period size: 165 Copynumber: 2.1 Consensus size: 165
35099 AAATTTACGC
35109 AATTTTATGCTATTTTACATTCAATACTTTGTATATAGTATTTTAATTTATTCCCTTTAATTTTC
1 AATTTTA-GCTA-TTTACATTCAATACTTTGTATATAGTATTTTAATTTATTCCCTTTAATTTTC
*
35174 AGCACATTAATTTTAGTCCTTTAAATTCTATATTTATTTTCTATGTTTTAATTTATACCTTATTT
64 AGCACATTAATTTTAGTCATTTAAATTCTATATTTATTTTCTATGTTTTAATTTATA-CTTATTT
35239 TCTATTTTCTTTCATTTTAGTCCTTTTATTAATATATTT
128 TCTATTTTCTTTCA-TTTAGTCCTTTTATTAATATATTT
35278 AATTTTAGCTATTT-CATTTCAATACTTTGGTATATAGTA-TTTAA-TTATT-CCTTTAATTTTC
1 AATTTTAGCTATTTACA-TTCAATACTTT-GTATATAGTATTTTAATTTATTCCCTTTAATTTTC
*
35339 AGCACATTAATTTTAGTTATTTAAATTCTAATATTTATTTTCTATGTTTTTTAATTTATA-TT-T
64 AGCACATTAATTTTAGTCATTTAAATTCT-ATATTTATTTTCTATG--TTTTAATTTATACTTAT
35402 TTTCT-TTTTCTTTTC-TTTAGTCCTTTTATTTAATATATTTT
126 TTTCTATTTTC-TTTCATTTAGTCCTTTTA-TTAATATA-TTT
35443 AATTTTAGCTATTT
1 AATTTTAGCTATTT
35457 TAACTTGGTT
Statistics
Matches: 169, Mismatches: 2, Indels: 20
0.88 0.01 0.10
Matches are distributed among these distances:
163 13 0.08
164 13 0.08
165 66 0.39
166 25 0.15
167 19 0.11
168 26 0.15
169 7 0.04
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.59
Consensus pattern (165 bp):
AATTTTAGCTATTTACATTCAATACTTTGTATATAGTATTTTAATTTATTCCCTTTAATTTTCAG
CACATTAATTTTAGTCATTTAAATTCTATATTTATTTTCTATGTTTTAATTTATACTTATTTTCT
ATTTTCTTTCATTTAGTCCTTTTATTAATATATTT
Found at i:37518 original size:20 final size:20
Alignment explanation
Indices: 37495--37544 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
37485 GCAAAAGTGG
37495 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
37515 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
37535 ATTTTGAAAA
1 ATTTTGAAAA
37545 AGGATTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATGAA
Found at i:40208 original size:93 final size:94
Alignment explanation
Indices: 40069--40256 Score: 353
Period size: 93 Copynumber: 2.0 Consensus size: 94
40059 GTGACGTACT
40069 GAAACATATCACAAGCTAAATTTTCCTTATTAAGTAAATATTAAAAAGATAAATTATATGTTTAG
1 GAAACATATCACAAGCTAAATTTTCCTTATTAAGTAAATATTAAAAAGATAAA-TATATGTTTAG
40134 TA-TTACACTATCATTTTTATTTCGTTTTA
65 TATTTACACTATCATTTTTATTTCGTTTTA
40163 GAAACATATCACAAGCTAAA-TTTCCTTATTAAGTAAATATTAAAAAGATAAATATATGTTTAGT
1 GAAACATATCACAAGCTAAATTTTCCTTATTAAGTAAATATTAAAAAGATAAATATATGTTTAGT
40227 ATTTACACTATCATTTTTATTTCGTTTTA
66 ATTTACACTATCATTTTTATTTCGTTTTA
40256 G
1 G
40257 TGCTTAAACT
Statistics
Matches: 93, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
92 13 0.14
93 60 0.65
94 20 0.22
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (94 bp):
GAAACATATCACAAGCTAAATTTTCCTTATTAAGTAAATATTAAAAAGATAAATATATGTTTAGT
ATTTACACTATCATTTTTATTTCGTTTTA
Found at i:41105 original size:19 final size:19
Alignment explanation
Indices: 41077--41115 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41067 ACCCTAAATT
* *
41077 TAAATTATTTAAAATTAAA
1 TAAATAATTTAAAAATAAA
41096 TAAATAATTTAAAAATAAA
1 TAAATAATTTAAAAATAAA
41115 T
1 T
41116 TATTTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATAATTTAAAAATAAA
Found at i:44610 original size:2 final size:2
Alignment explanation
Indices: 44605--44629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44595 AGTGTGTGGG
44605 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
44630 GAGTGAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:51939 original size:20 final size:20
Alignment explanation
Indices: 51914--51966 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
51904 TTTTACCCTG
*
51914 AGTATCGATACTCTAGGGGT
1 AGTATCGATACTCTAGGGGC
51934 AGTATCGATACTCTAGGGGC
1 AGTATCGATACTCTAGGGGC
51954 AGTATCGATACTC
1 AGTATCGATACTC
51967 CCCCTAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTCTAGGGGC
Found at i:55402 original size:60 final size:60
Alignment explanation
Indices: 55309--55422 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
55299 CAATTTGGGG
* * *
55309 AAAGGGTTTTGAAACCTCTAAGAGAGTTTCGAAACCTTTA-TGCATTATGTCATTCTGGAC
1 AAAGGGTTTTGAAACCCCTAAGAGAGTTTCGAAACCTGTATTGCATAAT-TCATTCTGGAC
*
55369 AAAGGGTTTTGAAACCAACCT-AG-GGGTTTCGAAACCTGTATTGCATAATTCATT
1 AAAGGGTTTTGAAACC--CCTAAGAGAGTTTCGAAACCTGTATTGCATAATTCATT
55423 TCTTCACCCG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
60 36 0.77
61 9 0.19
62 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (60 bp):
AAAGGGTTTTGAAACCCCTAAGAGAGTTTCGAAACCTGTATTGCATAATTCATTCTGGAC
Found at i:59186 original size:3 final size:3
Alignment explanation
Indices: 59180--59228 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
59170 TGTTATAATA
* * * *
59180 ATT ATT ATT ATT ATA ATT ATA ATA ATT ATT ATT ATT AAT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
59226 ATT
1 ATT
59229 TAATATTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:60562 original size:34 final size:34
Alignment explanation
Indices: 60509--60593 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
60499 TAAGTATTTT
*
60509 TATTTA-TTTTATTGCTTTTAAATATA-TAGTTCTA
1 TATTTATTTTTATT-ATTTTAAATATACTAGTT-TA
* * *
60543 -ATTGTATTTTTATTATTTTAATTTTACTTGTTTA
1 TATT-TATTTTTATTATTTTAAATATACTAGTTTA
60577 TATTTATTTTTATTATT
1 TATTTATTTTTATTATT
60594 ATTATGTAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 3 0.07
34 26 0.60
35 14 0.33
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.66
Consensus pattern (34 bp):
TATTTATTTTTATTATTTTAAATATACTAGTTTA
Found at i:72206 original size:3 final size:3
Alignment explanation
Indices: 72188--72263 Score: 62
Period size: 3 Copynumber: 25.0 Consensus size: 3
72178 TATAATATTA
* * * * * *
72188 AAT AAT ATAT ATT AAT AAT TAT TAT TAT TAT AAT TAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
72234 AAT AAT TAT AAT TAT AAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
72264 TATTATTATA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (3 bp):
AAT
Found at i:72216 original size:6 final size:6
Alignment explanation
Indices: 72208--72274 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
72198 ATTAATAATT
* * * * *
72208 ATTATT ATTATA ATTATA ATAATA ATAATA ATTATA ATTATA ATAATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA
* *
72256 ATAATA ATTATT ATTATA A
1 ATTATA ATTATA ATTATA A
72275 CATAAAAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:72227 original size:24 final size:24
Alignment explanation
Indices: 72177--72274 Score: 116
Period size: 24 Copynumber: 4.2 Consensus size: 24
72167 ATTTTGGGTT
72177 TTATAAT-ATTA-AATAA-TAT-A
1 TTATAATAATTATAATAATTATAA
* *
72197 -TATTAATAATTATTATTATTATAA
1 TTA-TAATAATTATAATAATTATAA
*
72221 TTATAATAATAATAATAATTATAA
1 TTATAATAATTATAATAATTATAA
*
72245 TTATAATAATTATAATAATTATTA
1 TTATAATAATTATAATAATTATAA
72269 TTATAA
1 TTATAA
72275 CATAAAAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
19 2 0.03
20 4 0.06
21 4 0.06
22 3 0.05
23 3 0.05
24 47 0.72
25 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTATAATAATTATAATAATTATAA
Found at i:72647 original size:17 final size:17
Alignment explanation
Indices: 72622--72682 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
72612 AAGGTTGAAC
72622 AAATTCTTCTCATTATG
1 AAATTCTTCTCATTATG
* *
72639 AATTTCTTCTTTCA-AATG
1 AAATTCTTC--TCATTATG
*
72657 -AGTTCTTCTCATTATG
1 AAATTCTTCTCATTATG
72673 AAATTCTTCT
1 AAATTCTTCT
72683 TCTTCAGATG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 23 0.66
18 3 0.09
19 3 0.09
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (17 bp):
AAATTCTTCTCATTATG
Found at i:72666 original size:34 final size:35
Alignment explanation
Indices: 72625--72715 Score: 118
Period size: 34 Copynumber: 2.7 Consensus size: 35
72615 GTTGAACAAA
*
72625 TTCTTCTCATTATGAATTTCTTCT-TTCAAATGAG
1 TTCTTCTCATTATGAAATTCTTCTCTTCAAATGAG
*
72659 TTCTTCTCATTATGAAATTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAAATTCTTC-TCTTCAAATGAG
*
72695 TTC-T-T-ATTATGAACTTCTTCT
1 TTCTTCTCATTATGAAATTCTTCT
72716 GGAAAAGCTG
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.02
33 14 0.27
34 23 0.44
35 2 0.04
36 12 0.23
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.51
Consensus pattern (35 bp):
TTCTTCTCATTATGAAATTCTTCTCTTCAAATGAG
Found at i:72828 original size:141 final size:138
Alignment explanation
Indices: 72538--72790 Score: 334
Period size: 141 Copynumber: 1.8 Consensus size: 138
72528 ATGAACTTTC
* * * *
72538 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGA
1 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGA
*
72603 ATTTGAACAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCAAATGAGTTCTTCTCA
66 ATTTGAACAAAGGTTGAACAAACTCTTCTCATTATGAATTTCTTCTTTCAAATGAGTTCTTCTCA
72668 TTATGAAA
131 TTATGAAA
72676 TTCTTCTTCTTCAGATGAGTTC-T-T-ATTATGAAC-TTCTTCTGGAAAAGCTGATCCATCAAGT
1 ----TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGCTGATCCATCAAGT
* * * *
72737 GATGGATTTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT
61 GAT-GAATTTGAAC-AAAGGTTGAACAAACTCTTCTCATTATGAATTTCTTCTT
72791 CCTTCTTCAG
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
138 3 0.03
139 32 0.32
140 9 0.09
141 37 0.37
142 18 0.18
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (138 bp):
TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGA
ATTTGAACAAAGGTTGAACAAACTCTTCTCATTATGAATTTCTTCTTTCAAATGAGTTCTTCTCA
TTATGAAA
Found at i:72912 original size:113 final size:113
Alignment explanation
Indices: 72660--73311 Score: 1061
Period size: 113 Copynumber: 5.8 Consensus size: 113
72650 TCAAATGAGT
* *
72660 TCTTCTCATTATGAA---ATTCTT-CTTCTTCAGATGAGTTC-T-T-ATTATGAACTTCTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
72718 AAAAGCTGATCCATCA-AGTGATGGATTTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAGA-TGATGGA-TTTGAGCAAAAGGTTGAACAAGC
* * **
72767 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTAA
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
**
72832 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
* *
72880 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTAG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
**
72945 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
* *
72993 TCTTCTCATTATGAATTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
73058 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
* *
73106 TCTTCTCATCATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
73171 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
*
73219 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
73284 AAAAGCTGATCCATCA-AGTGATGGATTT
66 AAAAGCTGATCCATCAGA-TGATGGATTT
73312 AAATCTTTGC
Statistics
Matches: 516, Mismatches: 20, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
107 15 0.03
110 5 0.01
111 17 0.03
112 2 0.00
113 437 0.85
114 39 0.08
115 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
AAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:73692 original size:52 final size:52
Alignment explanation
Indices: 73609--73713 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
73599 CAACATGTTA
* *
73609 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATAAAGTGATCTTTCAAAATGATTTCAC
73661 ATTCTGATAACAACTCATCTGATTATAAAGTGATCTTTCAAAATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATAAAGTGATCTTTCAAAATGATTTCAC
73713 A
1 A
73714 GATATCGATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (52 bp):
ATTCTGATAACAACTCATCTGATTATAAAGTGATCTTTCAAAATGATTTCAC
Found at i:74352 original size:83 final size:83
Alignment explanation
Indices: 74204--74601 Score: 539
Period size: 83 Copynumber: 4.7 Consensus size: 83
74194 GGTTTCATAT
* * ** *
74204 CAAACCAGATCAGATAACTCAAAGAACCCTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
74269 TTCAATAACTGGTTTTAC
66 TTCAATAACTGGTTTTAC
*
74287 CAAACCAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
* *
74352 TTCAATGATTGGTTTTAC
66 TTCAATAACTGGTTTTAC
74370 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC-ATTGAGCACATTTATCTTTCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTTATCTTTCAA
74434 ATTCAATAACTGGTTCTGTGGTTCATAC
65 ATTCAATAACT-G----GT--TT--TAC
* **
74462 CAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT-TTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTT-CAA
* * *
74526 ATTCAATGATTGATTTTAC
65 ATTCAATAACTGGTTTTAC
* *
74545 CAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACATTTAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTAT
74602 TGTTCCAGTT
Statistics
Matches: 282, Mismatches: 21, Indels: 24
0.86 0.06 0.07
Matches are distributed among these distances:
82 1 0.00
83 201 0.71
84 1 0.00
85 2 0.01
87 1 0.00
88 2 0.01
90 2 0.01
91 4 0.01
92 67 0.24
93 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
TTCAATAACTGGTTTTAC
Found at i:74534 original size:175 final size:166
Alignment explanation
Indices: 74204--74601 Score: 568
Period size: 175 Copynumber: 2.3 Consensus size: 166
74194 GGTTTCATAT
* **
74204 CAAACCAGATCAGATAACTCAAAGAACCCTTCCAGAAGATGCTATT-AGCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC-ATTGAGCACATTTATCTTCCAA
* *
74268 ATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATG
65 ATTCAATAACTGGTTTTACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
74333 AGCACATTTATCTTTCAAATTCAATGATTGGTTTTAC
130 AGCACATTCATCTTTCAAATTCAATGATTGATTTTAC
*
74370 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCATTGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCATTGAGCACATTTATCTTCCAAA
74435 TTCAATAACTGGTTCTGTGGTTCATACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 TTCAATAACT-G----GT--TT--TACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
74500 ATGCTATGAGCACATTCCT-TTTCCAAATTCAATGATTGATTTTAC
122 ATGCTATGAGCACATTCATCTTT-CAAATTCAATGATTGATTTTAC
* *
74545 CAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGC-TATGAGCACATTTAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAT-TGAGCACATTTAT
74602 TGTTCCAGTT
Statistics
Matches: 209, Mismatches: 11, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
165 3 0.01
166 67 0.32
167 1 0.00
171 2 0.01
173 2 0.01
174 4 0.02
175 130 0.62
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (166 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCATTGAGCACATTTATCTTCCAAA
TTCAATAACTGGTTTTACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTTCAAATTCAATGATTGATTTTAC
Found at i:75774 original size:24 final size:23
Alignment explanation
Indices: 75744--75814 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
75734 TGACCCCCCC
75744 TTTTTTCTTCTTCTTTTTTCTCTT
1 TTTTTTCTT-TTCTTTTTTCTCTT
*
75768 TTTTTTCTTTTTTACTTTTTCTC-T
1 TTTTTTCTTTTCT--TTTTTCTCTT
75792 TTTTTTCTTTT-TCTTTTTCTCTT
1 TTTTTTCTTTTCT-TTTTTCTCTT
75815 CAAGCATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 9 0.21
23 5 0.12
24 21 0.49
25 8 0.19
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTTCTTTTTTCTCTT
Found at i:75788 original size:14 final size:15
Alignment explanation
Indices: 75768--75809 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
75758 TTTTTCTCTT
75768 TTTTTTCTTTTTTAC
1 TTTTTTCTTTTTTAC
*
75783 TTTTTCTCTTTTTTTC
1 TTTTT-TCTTTTTTAC
75799 -TTTTTCTTTTT
1 TTTTTTCTTTTT
75810 CTCTTCAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 9 0.36
16 9 0.36
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTTTTTAC
Found at i:75814 original size:8 final size:8
Alignment explanation
Indices: 75743--75814 Score: 64
Period size: 8 Copynumber: 9.4 Consensus size: 8
75733 TTGACCCCCC
75743 CTTTTT-T
1 CTTTTTCT
*
75750 CTTCTTCT
1 CTTTTTCT
75758 -TTTTTCT
1 CTTTTTCT
*
75765 CTTTTTTTT
1 C-TTTTTCT
75774 CTTTTT-T
1 CTTTTTCT
75781 ACTTTTTCT
1 -CTTTTTCT
*
75790 CTTTTTTT
1 CTTTTTCT
75798 C-TTTT-T
1 CTTTTTCT
75804 CTTTTTCT
1 CTTTTTCT
75812 CTT
1 CTT
75815 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
6 2 0.04
7 20 0.37
8 24 0.44
9 8 0.15
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (8 bp):
CTTTTTCT
Found at i:83136 original size:15 final size:15
Alignment explanation
Indices: 83113--83144 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
83103 TGAAATGAAT
83113 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
83128 AATGCATGTATGCAA
1 AATGAATGTATGCAA
83143 AA
1 AA
83145 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:92804 original size:37 final size:36
Alignment explanation
Indices: 92746--92819 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
92736 AAGTTTACAG
*
92746 AATATGACAACACATCTAAATTTATAAAAAGATGACA
1 AATATGACAACACATCCAAATTTAT-AAAAGATGACA
* *
92783 AATATGACAACATATCCAAATTTATACAAGATGACA
1 AATATGACAACACATCCAAATTTATAAAAGATGACA
92819 A
1 A
92820 TATTTTCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 11 0.32
37 23 0.68
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.24
Consensus pattern (36 bp):
AATATGACAACACATCCAAATTTATAAAAGATGACA
Found at i:93401 original size:16 final size:16
Alignment explanation
Indices: 93380--93425 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
93370 GAATCTATGA
93380 AGGAATTGAAATCTGT
1 AGGAATTGAAATCTGT
*
93396 AGGAATTGAAATTTGT
1 AGGAATTGAAATCTGT
*
93412 AGGAATTGGAATCT
1 AGGAATTGAAATCT
93426 CAATCTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (16 bp):
AGGAATTGAAATCTGT
Found at i:93987 original size:28 final size:29
Alignment explanation
Indices: 93921--93990 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 29
93911 CCCTAAACCC
*
93921 AAACCCGACCCGAATATCACACTTAAAAA
1 AAACCCGACCCGAATATCAAACTTAAAAA
93950 AATTCGACCCGACCCGAATATCAAACTT-AAAA
1 AA----ACCCGACCCGAATATCAAACTTAAAAA
93982 AAACCCGAC
1 AAACCCGAC
93991 ATGACCTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
28 7 0.19
29 2 0.06
32 6 0.17
33 21 0.58
ACGTcount: A:0.46, C:0.31, G:0.09, T:0.14
Consensus pattern (29 bp):
AAACCCGACCCGAATATCAAACTTAAAAA
Found at i:97143 original size:74 final size:74
Alignment explanation
Indices: 97034--97179 Score: 265
Period size: 74 Copynumber: 2.0 Consensus size: 74
97024 GAAGAACTAA
* *
97034 CCAAGGAATTCCAATTCAAACAACAACATGGAAAATAGCAGCTAAAATGGTTTACAAGCTACAAC
1 CCAAGGAATTCCAATTCAAACAACAACATGGAAAATAGCAGCTAAAAAGGTTTACAAGCCACAAC
97099 TATCAAACC
66 TATCAAACC
*
97108 CCAAGGAATTCTAATTCAAACAACAACATGGAAAATAGCAGCTAAAAAGGTTTACAAGCCACAAC
1 CCAAGGAATTCCAATTCAAACAACAACATGGAAAATAGCAGCTAAAAAGGTTTACAAGCCACAAC
97173 TATCAAA
66 TATCAAA
97180 AGCTAACACC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.18
Consensus pattern (74 bp):
CCAAGGAATTCCAATTCAAACAACAACATGGAAAATAGCAGCTAAAAAGGTTTACAAGCCACAAC
TATCAAACC
Found at i:98578 original size:11 final size:11
Alignment explanation
Indices: 98562--98624 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
98552 GTATTAGAGA
98562 ATTTTTAATAT
1 ATTTTTAATAT
98573 ATTTTTAA-A-
1 ATTTTTAATAT
98582 ATTTTATAAT-T
1 ATTTT-TAATAT
***
98593 ATCAATAATAT
1 ATTTTTAATAT
98604 ATTTTTAATAT
1 ATTTTTAATAT
98615 ATTTTTAATA
1 ATTTTTAATA
98625 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:100644 original size:2 final size:2
Alignment explanation
Indices: 100637--100662 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
100627 ATTCAACCTT
100637 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
100663 ACACATCTAA
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):
TA
Found at i:102412 original size:4 final size:4
Alignment explanation
Indices: 102403--102439 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
102393 GAAAAAATAA
102403 AAAT AAAT AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
102440 AATTCCGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 4 0.13
4 27 0.87
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:102419 original size:22 final size:22
Alignment explanation
Indices: 102401--102442 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
102391 TTGAAAAAAT
102401 AAAAATAAATAAATAAAAATAA
1 AAAAATAAATAAATAAAAATAA
*
102423 ATAAATAAATAAATAAAAAT
1 AAAAATAAATAAATAAAAAT
102443 TCCGTTCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAATAAATAAATAAAAATAA
Found at i:102426 original size:18 final size:18
Alignment explanation
Indices: 102397--102442 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
102387 TACTTTGAAA
102397 AAATAAAAATAAATAAAT
1 AAATAAAAATAAATAAAT
102415 AAA-AATAAATAAATAAAT
1 AAATAA-AAATAAATAAAT
102433 AAATAAAAAT
1 AAATAAAAAT
102443 TCCGTTCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAAAATAAATAAAT
Found at i:102442 original size:14 final size:14
Alignment explanation
Indices: 102397--102439 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
102387 TACTTTGAAA
102397 AAATAAAAATAAAT
1 AAATAAAAATAAAT
102411 AAATAAAAATAAAT
1 AAATAAAAATAAAT
102425 AAAT--AAATAAAT
1 AAATAAAAATAAAT
102437 AAA
1 AAA
102440 AATTCCGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.38
14 18 0.62
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:103196 original size:22 final size:22
Alignment explanation
Indices: 103170--103278 Score: 200
Period size: 22 Copynumber: 5.0 Consensus size: 22
103160 GCATGTGAAA
*
103170 TATGTCCCGAAGGACCTGTGAG
1 TATGTCCCGAAGGACCTATGAG
103192 TATGTCCCGAAGGACCTATGAG
1 TATGTCCCGAAGGACCTATGAG
*
103214 TATGTCTCGAAGGACCTATGAG
1 TATGTCCCGAAGGACCTATGAG
103236 TATGTCCCGAAGGACCTATGAG
1 TATGTCCCGAAGGACCTATGAG
103258 TATGTCCCGAAGGACCTATGA
1 TATGTCCCGAAGGACCTATGA
103279 AACCCTCGAC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 84 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (22 bp):
TATGTCCCGAAGGACCTATGAG
Found at i:103774 original size:2 final size:2
Alignment explanation
Indices: 103745--103802 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
103735 TACCTAGATC
* * *
103745 AT AT A- AT AT AT TT CAT AT TT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103787 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
103803 CACTTCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107860 original size:2 final size:2
Alignment explanation
Indices: 107853--107884 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
107843 ATAGTTTAGT
107853 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
107885 CTAAACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109217 original size:29 final size:31
Alignment explanation
Indices: 109174--109232 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
109164 TATTTTATTA
**
109174 TATTTAATATTTTTTTTGTAATTTATTTAAG
1 TATTTAATATTTTTTTAATAATTTATTTAAG
*
109205 TATTTAA-A-TTTTTTAATATTTTATTTAA
1 TATTTAATATTTTTTTAATAATTTATTTAA
109233 TTAATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.68
30 1 0.04
31 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TATTTAATATTTTTTTAATAATTTATTTAAG
Found at i:109227 original size:17 final size:18
Alignment explanation
Indices: 109193--109225 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
109183 TTTTTTTTGT
109193 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
109211 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
109226 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:111041 original size:27 final size:27
Alignment explanation
Indices: 110978--111042 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
110968 ACCCGATGCT
*
110978 GCCGCCGCCACTTAGTTTTATGACCCC
1 GCCGCCGCCACTTAGTTTTATAACCCC
* *
111005 GCCACTGCCACTTAGTTTTATAACCCC
1 GCCGCCGCCACTTAGTTTTATAACCCC
111032 GCCGCCGCCAC
1 GCCGCCGCCAC
111043 CGTCACAGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (27 bp):
GCCGCCGCCACTTAGTTTTATAACCCC
Found at i:111602 original size:34 final size:33
Alignment explanation
Indices: 111535--111622 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 33
111525 TAATACTTAC
*
111535 TTTATTTCGTT-AATTTGGTTGGATTTATTTTAA
1 TTTATTTTGTTAAATTT-GTTGGATTTATTTTAA
111568 TTTATTTTGTTAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTGTTAAATTTGTTGGA-TTTATT-TTAA
* *
111602 TGTATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAAATTTGTT
111623 TATTACCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 18 0.38
34 19 0.40
35 11 0.23
ACGTcount: A:0.19, C:0.02, G:0.16, T:0.62
Consensus pattern (33 bp):
TTTATTTTGTTAAATTTGTTGGATTTATTTTAA
Found at i:114684 original size:21 final size:21
Alignment explanation
Indices: 114630--114692 Score: 90
Period size: 22 Copynumber: 3.0 Consensus size: 21
114620 GCATATGAAA
*
114630 TTATCTCGAAGGACCTGTGAG
1 TTATCTCGAAGGACCTATGAG
*
114651 TATGTCTCGAAGGACCTATGAG
1 T-TATCTCGAAGGACCTATGAG
*
114673 TTATCCCGAAGGACCTATGA
1 TTATCTCGAAGGACCTATGA
114693 AACCCTCGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (21 bp):
TTATCTCGAAGGACCTATGAG
Found at i:115321 original size:21 final size:21
Alignment explanation
Indices: 115295--115375 Score: 144
Period size: 21 Copynumber: 3.9 Consensus size: 21
115285 TTTCGTTCAA
*
115295 TGGGGGGTATCGGTACCCAGC
1 TGGGGGGTATCGATACCCAGC
115316 TGGGGGGTATCGATACCCAGC
1 TGGGGGGTATCGATACCCAGC
*
115337 TAGGGGGTATCGATACCCAGC
1 TGGGGGGTATCGATACCCAGC
115358 TGGGGGGTATCGATACCC
1 TGGGGGGTATCGATACCC
115376 TCAATACATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.19, C:0.23, G:0.38, T:0.20
Consensus pattern (21 bp):
TGGGGGGTATCGATACCCAGC
Found at i:115580 original size:21 final size:21
Alignment explanation
Indices: 115556--115595 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
115546 ACTCATTCCT
*
115556 ACTCAATAATCACT-TCCTTAA
1 ACTCAAAAAT-ACTATCCTTAA
115577 ACTCAAAAATACTATCCTT
1 ACTCAAAAATACTATCCTT
115596 TATATGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (21 bp):
ACTCAAAAATACTATCCTTAA
Found at i:119564 original size:2 final size:2
Alignment explanation
Indices: 119552--119584 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
119542 TTTATTTTAA
119552 AT AT A- AT 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 AT AT AT AT
119585 CCAACAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129063 original size:16 final size:15
Alignment explanation
Indices: 129042--129074 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
129032 AAAAATTAGT
129042 TAAATAATAATAATAA
1 TAAATAATAATAA-AA
129058 TAAATAATAATAAAA
1 TAAATAATAATAAAA
129073 TA
1 TA
129075 GAAAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATAATAATAAAA
Found at i:129090 original size:5 final size:5
Alignment explanation
Indices: 129077--129115 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
129067 ATAAAATAGA
129077 AAATAG AAATG AAATG AAATG AAATG AAATG AAATG AAA
1 AAAT-G AAATG AAATG AAATG AAATG AAATG AAATG AAA
129116 AAAATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:129130 original size:11 final size:11
Alignment explanation
Indices: 129114--129138 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
129104 AATGAAATGA
129114 AAAAAATAAAT
1 AAAAAATAAAT
129125 AAAAAATAAAT
1 AAAAAATAAAT
129136 AAA
1 AAA
129139 GAAGTGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:130433 original size:14 final size:15
Alignment explanation
Indices: 130416--130450 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
130406 GATAGAATTA
130416 ATAATATTATAT-AT
1 ATAATATTATATAAT
*
130430 ATAAAATTATATAAT
1 ATAATATTATATAAT
130445 ATAATA
1 ATAATA
130451 ATATTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATATTATATAAT
Found at i:130461 original size:17 final size:16
Alignment explanation
Indices: 130414--130462 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
130404 ATGATAGAAT
130414 TAATAATATTATATATA
1 TAATAATATTATA-ATA
130431 TAA-AAT-TATATAATA
1 TAATAATAT-TATAATA
130446 TAATAATATTACTAATA
1 TAATAATATTA-TAATA
130463 AAAGGACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.25
16 12 0.43
17 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATATTATAATA
Found at i:131173 original size:106 final size:106
Alignment explanation
Indices: 130989--131874 Score: 1273
Period size: 106 Copynumber: 8.5 Consensus size: 106
130979 GCATTGTTCC
* * ** *
130989 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
131053 ACCAGTC-GTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
131095 GAGTCCAATATGCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
131160 CCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
131201 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
**
131266 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
131307 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * ***
131372 CCAGCGGTCCCTTCGTCGTGAAGTTAAACATATATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
131413 GAGTCCAATATCCTTCGCTGTTAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
131478 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
131519 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
131584 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
131625 GAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAATTGTTTATTGACA
131689 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
131731 GAGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
131784 ACAGCGGTCCCCTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
131825 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AGAATTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAA
131875 GCCCCTTCGT
Statistics
Matches: 706, Mismatches: 57, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
94 78 0.11
95 3 0.00
96 1 0.00
99 3 0.00
100 4 0.01
101 3 0.00
104 2 0.00
105 5 0.01
106 606 0.86
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:131827 original size:94 final size:94
Alignment explanation
Indices: 131666--131859 Score: 334
Period size: 94 Copynumber: 2.1 Consensus size: 94
131656 TTGACTCTAG
* * *
131666 AATTGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1 AATTGGAAAATTGTTTATTGACAAACAGCGGTCCCCTCATCGTGAAGTTGAACTTGCGTTGTCTG
*
131731 GAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GAGTCCAATATCCTTCGCTGTGAAGTTGA
* *
131760 AATTGGGAAATTGTTTATTGACAAACAGCGGTCCCCTCATCGTGAAGTTGAACTTGTGTTGTCTG
1 AATTGGAAAATTGTTTATTGACAAACAGCGGTCCCCTCATCGTGAAGTTGAACTTGCGTTGTCTG
131825 GAGTCCAATATCCTTCGCTGTGAAGTTGA
66 GAGTCCAATATCCTTCGCTGTGAAGTTGA
131854 AATTGG
1 AATTGG
131860 CTCTAGAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (94 bp):
AATTGGAAAATTGTTTATTGACAAACAGCGGTCCCCTCATCGTGAAGTTGAACTTGCGTTGTCTG
GAGTCCAATATCCTTCGCTGTGAAGTTGA
Found at i:136047 original size:10 final size:10
Alignment explanation
Indices: 136021--136053 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
136011 AAAAATTAGT
*
136021 TAAATAATAG
1 TAAATAATAA
136031 T-AATAATAA
1 TAAATAATAA
136040 TAAATAATAA
1 TAAATAATAA
136050 TAAA
1 TAAA
136054 ATAGAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (10 bp):
TAAATAATAA
Found at i:136098 original size:11 final size:11
Alignment explanation
Indices: 136082--136106 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
136072 ATGAAATGAA
136082 AAAAAATAAAT
1 AAAAAATAAAT
136093 AAAAAATAAAT
1 AAAAAATAAAT
136104 AAA
1 AAA
136107 GAAGTGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:136103 original size:15 final size:15
Alignment explanation
Indices: 136038--136106 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
136028 TAGTAATAAT
136038 AATAAAT-AATAATAA
1 AATAAATAAATAA-AA
* *
136053 AATAGA-AAAT-AGA
1 AATAAATAAATAAAA
*
136066 AATGAAATGAAATGAAA
1 AAT-AAAT-AAATAAAA
136083 AA-AAATAAATAAAA
1 AATAAATAAATAAAA
136097 AATAAATAAA
1 AATAAATAAA
136107 GAAGTGGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 4 0.09
14 12 0.28
15 19 0.44
16 4 0.09
17 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (15 bp):
AATAAATAAATAAAA
Found at i:139844 original size:13 final size:14
Alignment explanation
Indices: 139812--139845 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
139802 TTAATATTTT
139812 TTTATATTTTAAACA
1 TTTA-ATTTTAAACA
139827 TTTAATTTTAAA-A
1 TTTAATTTTAAACA
139840 TTTAAT
1 TTTAAT
139846 AAAATTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 8 0.42
15 4 0.21
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATTTTAAACA
Found at i:140622 original size:20 final size:20
Alignment explanation
Indices: 140597--140802 Score: 92
Period size: 20 Copynumber: 10.1 Consensus size: 20
140587 AATGACCAAT
140597 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
140617 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
140637 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
140657 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
** *
140678 AAGTTCGCAATGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
140701 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
140721 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
140741 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
140761 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
140781 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
140801 AA
1 AA
140803 GAAAATCGCA
Statistics
Matches: 146, Mismatches: 32, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
20 118 0.81
21 13 0.09
23 15 0.10
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:140755 original size:40 final size:40
Alignment explanation
Indices: 140682--140830 Score: 165
Period size: 40 Copynumber: 3.6 Consensus size: 40
140672 GCTTCCAAGT
*
140682 TCGCAATGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAATGCGA-TT-G-AGAGAATCGCAATGCGATTGATAGAA
* * *
140725 TCGCAATGCGATTGATAGAATCGCAATGCGATTTATATAA
1 TCGCAATGCGATTGAGAGAATCGCAATGCGATTGATAGAA
* *
140765 TCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGA-AGAAAA
1 TCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-GATAG--AA
*
140808 TCGCAATGCGACTGAGAGAATCG
1 TCGCAATGCGATTGAGAGAATCG
140831 TAACGTTGAA
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
40 50 0.55
41 4 0.04
42 3 0.03
43 34 0.37
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGATTGAGAGAATCGCAATGCGATTGATAGAA
Found at i:140954 original size:6 final size:6
Alignment explanation
Indices: 140943--140998 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
140933 GACACGTATT
140943 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
140991 ACC-CG ACC
1 ACCACG ACC
140999 CGAGACGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Done.