Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001660.1 Hibiscus syriacus cultivar Beakdansim tig00003318_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: 100866
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1484 original size:16 final size:17
Alignment explanation
Indices: 1460--1492 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1450 TTGCTCAAGG
1460 ATAACTTAAA-AAATTA
1 ATAACTTAAATAAATTA
*
1476 ATAATTTAAATAAATTA
1 ATAACTTAAATAAATTA
1493 TAAAAAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAACTTAAATAAATTA
Found at i:1593 original size:28 final size:27
Alignment explanation
Indices: 1525--1586 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
1515 CAAATATTAT
*
1525 TAAAAATAAAAATAGAGTTTGATTAAC
1 TAAAAATAAAAATAGAGTTCGATTAAC
* *
1552 TAAAAAAAGAAAATGGAGTTCGATTAAC
1 TAAAAATA-AAAATAGAGTTCGATTAAC
1580 TAAAAAT
1 TAAAAAT
1587 TACAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (27 bp):
TAAAAATAAAAATAGAGTTCGATTAAC
Found at i:5845 original size:14 final size:15
Alignment explanation
Indices: 5821--5850 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5811 AAATTTCAAT
5821 ATTATAAATAAATAA
1 ATTATAAATAAATAA
5836 ATTA-AAATAAATAA
1 ATTATAAATAAATAA
5850 A
1 A
5851 CATAGATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTATAAATAAATAA
Found at i:6348 original size:34 final size:34
Alignment explanation
Indices: 6291--6375 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
6281 ATACCCTTTT
*
6291 AAATAAATAAATAAATAAATAAATAAAGTATTTG
1 AAATAAATAAATAAATAAATAAATAAAGTATTCG
* * * *
6325 AAATAAATGAATACATAATTAAATAAATTATTCG
1 AAATAAATAAATAAATAAATAAATAAAGTATTCG
6359 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
6376 CTTTAGAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (34 bp):
AAATAAATAAATAAATAAATAAATAAAGTATTCG
Found at i:6395 original size:4 final size:4
Alignment explanation
Indices: 6290--6375 Score: 73
Period size: 4 Copynumber: 20.5 Consensus size: 4
6280 CATACCCTTT
** * *
6290 TAAA TAAA TAAA TAAA TAAA TAAA TAAA GTATT TGAAA TAAA TGAA TACA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA T-AAA TAAA TAAA TAAA
* * *
6340 TAAT TAAA TAAA TTAT TCGAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA T--AAA TAAA TAAA TAAA TA
6376 CTTTAGAGTA
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
4 58 0.91
5 4 0.06
6 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:7409 original size:6 final size:6
Alignment explanation
Indices: 7392--7448 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
7382 TCTCGTCTCG
* * *
7392 GGTCTT GGTCGT GATCGT GGTCGT GGTCGT GATCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
7440 GGTCGT GGT
1 GGTCGT GGT
7449 AATACGTGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.04, C:0.16, G:0.46, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:7418 original size:18 final size:18
Alignment explanation
Indices: 7392--7448 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
7382 TCTCGTCTCG
*
7392 GGTCTTGGTCGTGATCGT
1 GGTCGTGGTCGTGATCGT
7410 GGTCGTGGTCGTGATCGT
1 GGTCGTGGTCGTGATCGT
*
7428 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGATCGT
7446 GGT
1 GGT
7449 AATACGTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.04, C:0.16, G:0.46, T:0.35
Consensus pattern (18 bp):
GGTCGTGGTCGTGATCGT
Found at i:7660 original size:21 final size:21
Alignment explanation
Indices: 7538--7652 Score: 178
Period size: 21 Copynumber: 5.5 Consensus size: 21
7528 CGTTGCGATT
* *
7538 TTGGACTATCGCAACGCGAAT
1 TTGGACTATCGCAATGCGAAC
7559 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
7580 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
7601 TTGGATTATC-CTAATGCGAAC
1 TTGGACTATCGC-AATGCGAAC
7622 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
7643 TTCGACTATC
1 TTGGACTATC
7653 ACATTGCGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
20 1 0.01
21 85 0.98
22 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:7696 original size:21 final size:21
Alignment explanation
Indices: 7625--7700 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
7615 TGCGAACTTG
* *
7625 GACTATCGCAATGCGA-ACTTC
1 GACTATCGCATTGCGATA-GTC
* *
7646 GACTATCACATTGCGGTAGTCC
1 GACTATCGCATTGCGATAGT-C
* *
7668 AAGT-TCGCATTGCGATAGTC
1 GACTATCGCATTGCGATAGTC
7688 GACTATCGCATTG
1 GACTATCGCATTG
7701 TGATTTACAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
20 3 0.07
21 35 0.83
22 4 0.10
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:7754 original size:21 final size:21
Alignment explanation
Indices: 7728--7850 Score: 153
Period size: 21 Copynumber: 5.9 Consensus size: 21
7718 TTGCTCACAA
7728 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
7749 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* *
7770 TGCGATAGT-CGACTATCGCAT
1 TGCGATAGTCCAAGT-TCGCAT
* *
7791 TGCGAT-TTACATA-TTCGCAT
1 TGCGATAGTCCA-AGTTCGCAT
*
7811 TGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
*
7832 TGCGATAGTCGAAGTTCGC
1 TGCGATAGTCCAAGTTCGC
7851 GTTATGAATC
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
20 17 0.19
21 72 0.80
22 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCAT
Found at i:10532 original size:17 final size:17
Alignment explanation
Indices: 10493--10564 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
10483 ATTCATGCAT
*
10493 CTAGTTCATTTAATAAAA
1 CTAGTTCA-TTAATTAAA
*
10511 TTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
* * *
10528 CTAGTCCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
10545 CTAGTTAATTTATTAAA
1 CTAGTTCATTAATTAAA
10562 CTA
1 CTA
10565 ACACTGAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 37 0.84
18 7 0.16
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:16590 original size:17 final size:17
Alignment explanation
Indices: 16570--16620 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
16560 TTAATAAAGT
16570 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
16587 TAG-TCTATTCATCAAAC
1 TAGTTC-ATTAATTAAAC
* *
16604 TAGTTAATTTATTAAAC
1 TAGTTCATTAATTAAAC
16621 AATTCTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 2 0.07
17 24 0.89
18 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:23729 original size:15 final size:15
Alignment explanation
Indices: 23701--23838 Score: 169
Period size: 15 Copynumber: 9.2 Consensus size: 15
23691 TAATAAGCTT
*
23701 ATTTA-TTTACAATA
1 ATTTATTTTAAAATA
23715 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
23730 A-TT-TTATAAAATA
1 ATTTATTTTAAAATA
23743 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
23758 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
23773 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
23788 ATTTATTATAAAATGGA
1 ATTTATTTTAAAAT--A
23805 TTGATTTATTTT-AAATA
1 ---ATTTATTTTAAAATA
23822 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
23836 ATT
1 ATT
23839 ATTAGTATGG
Statistics
Matches: 111, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.09
14 26 0.23
15 61 0.55
17 2 0.02
19 4 0.04
20 8 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:23860 original size:31 final size:32
Alignment explanation
Indices: 23822--23897 Score: 129
Period size: 31 Copynumber: 2.4 Consensus size: 32
23812 ATTTTAAATA
23822 ATTTATTTTAAATAATT-ATTAGTATGGATTG
1 ATTTATTTTAAATAATTAATTAGTATGGATTG
23853 ATTTATTTTAAATAATTAATTAGTATGGATTG
1 ATTTATTTTAAATAATTAATTAGTATGGATTG
*
23885 ATTT-TTTAAAATA
1 ATTTATTTTAAATA
23898 TGAATTGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 25 0.58
32 18 0.42
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (32 bp):
ATTTATTTTAAATAATTAATTAGTATGGATTG
Found at i:23937 original size:78 final size:80
Alignment explanation
Indices: 23843--23991 Score: 257
Period size: 78 Copynumber: 1.9 Consensus size: 80
23833 ATAATTATTA
23843 GTATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGA-TT-TTTTAAAATATGAATTGA
1 GTATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTTATTTTAAAATATGAATTGA
23906 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
* * *
23921 GTATTGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTTATTTTAAAATATGAATTGA
23986 TTTATT
66 TTTATT
23992 TTAAATAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 41 0.62
79 2 0.03
80 23 0.35
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (80 bp):
GTATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTTATTTTAAAATATGAATTGA
TTTATTATTGTAGTT
Found at i:23979 original size:22 final size:22
Alignment explanation
Indices: 23954--24049 Score: 93
Period size: 22 Copynumber: 4.0 Consensus size: 22
23944 AATTTATTAG
23954 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
23976 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
*
24000 TTATTAGTATTGATTGATTTATTTTAAAA
1 -TA-T-GGATTGA----TTTATTTTAAAA
*
24029 TATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
24050 TAATTTATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
22 29 0.46
23 2 0.03
24 2 0.03
25 2 0.03
26 7 0.11
27 7 0.11
28 2 0.03
29 2 0.03
30 2 0.03
31 8 0.13
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:24018 original size:31 final size:31
Alignment explanation
Indices: 23976--24180 Score: 170
Period size: 31 Copynumber: 6.7 Consensus size: 31
23966 TATTTTAAAA
23976 TATGGATTGATTTATTTTAAATAATTATTAG
1 TATGGATTGATTTATTTTAAATAATTATTAG
*
24007 TATTGATTGATTTATTTT-AA-AA-TA-T-G
1 TATGGATTGATTTATTTTAAATAATTATTAG
24033 -A---ATTGATTTATTTTAAATAATTTATTA-
1 TATGGATTGATTTATTTTAAATAA-TTATTAG
24060 TATGGATTGATTTATTTT--A-AA-TATTAG
1 TATGGATTGATTTATTTTAAATAATTATTAG
24087 TATGGATTGATTTATTTTAAAATAATTGATTTATTTTG
1 TATGGATTGATTTATTTT-AAATAATT-A-TTA----G
* *
24125 TAGTTGTATAGATTTATTTTAAATAATT-TATAG
1 TA--TGGATTGATTTATTTTAAATAATTAT-TAG
*
24158 TATGGATTGATTTATTTAAAATA
1 TATGGATTGATTTATTTTAAATA
24181 TGGATGATTT
Statistics
Matches: 143, Mismatches: 6, Indels: 50
0.72 0.03 0.25
Matches are distributed among these distances:
22 13 0.09
23 2 0.01
24 2 0.01
25 1 0.01
26 8 0.06
27 20 0.14
28 5 0.03
29 3 0.02
30 3 0.02
31 50 0.35
32 1 0.01
33 4 0.03
34 3 0.02
36 1 0.01
37 2 0.01
38 3 0.02
39 8 0.06
40 14 0.10
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (31 bp):
TATGGATTGATTTATTTTAAATAATTATTAG
Found at i:24022 original size:53 final size:54
Alignment explanation
Indices: 23926--24113 Score: 290
Period size: 53 Copynumber: 3.4 Consensus size: 54
23916 TAGTTGTATT
23926 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
*
23980 GATTGATTTATTTTAAATAA-TTATTAGTATTGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
*
24033 AATTGATTTATTTTAAATAATTTATTA-TATGGATTGATTTATTTTAAATATTAGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-A--A-TATG
24091 GATTGATTTATTTTAAAATAATT
1 GATTGATTTATTTT-AAATAATT
24114 GATTTATTTT
Statistics
Matches: 123, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
53 68 0.55
54 28 0.23
55 1 0.01
57 1 0.01
58 17 0.14
59 8 0.07
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
Found at i:24117 original size:23 final size:26
Alignment explanation
Indices: 23948--24354 Score: 129
Period size: 27 Copynumber: 16.1 Consensus size: 26
23938 TTAAATAATT
23948 TATTAGTATGGATTGATTTATTTTAAA
1 TATTAG-ATGGATTGATTTATTTTAAA
23975 -A-T--ATGGATTGATTTATTTTAAATAA
1 TATTAGATGGATTGATTTATTTT--A-AA
*
24000 TTATTAGTATTGATTGATTTATTTTAAA
1 -TATTAG-ATGGATTGATTTATTTTAAA
*
24028 -A-T--ATGAATTGATTTATTTTAAATAA
1 TATTAGATGGATTGATTTATTTT--A-AA
*
24053 TTTATTATATGGATTGATTTATTTTAAA
1 --TATTAGATGGATTGATTTATTTTAAA
24081 TATTAGTATGGATTGATTTATTTTAAA
1 TATTAG-ATGGATTGATTTATTTTAAA
*
24108 -A-T--A---ATTGATTTATTTT--G
1 TATTAGATGGATTGATTTATTTTAAA
* * **
24125 TAGTT-GTATAGATTTA-TT-TTAAATAA
1 TA-TTAG-ATGGATTGATTTATTTTA-AA
*
24151 TTTATAGTATGGATTGATTTA-TTTAAA
1 TAT-TAG-ATGGATTGATTTATTTTAAA
24178 -A-T--ATGGA-TGATTT-TTTTAAA
1 TATTAGATGGATTGATTTATTTTAAA
* * *
24198 TAATTTTAGTTGTATTGATTTGTTTTAAA
1 T-A--TTAGATGGATTGATTTATTTTAAA
24227 TATTTATTTGTATGGATTGATTTATTTT-AA
1 TA-TTA---G-ATGGATTGATTTATTTTAAA
**
24257 -A-T--ATGGATTGATTTA--TTATG
1 TATTAGATGGATTGATTTATTTTAAA
24277 TAGTT-GTATGGATTGATTTATTTTAAA
1 TA-TTAG-ATGGATTGATTTATTTTAAA
* *
24304 TAATTTA-TTAGATTGATTTATTTTAAA
1 T-A-TTAGATGGATTGATTTATTTTAAA
24331 -A-T--ATGGATTGATTTATTTTAAA
1 TATTAGATGGATTGATTTATTTTAAA
24353 TA
1 TA
24355 ATTATTATTG
Statistics
Matches: 291, Mismatches: 30, Indels: 122
0.66 0.07 0.28
Matches are distributed among these distances:
18 1 0.00
19 15 0.05
20 13 0.04
21 19 0.07
22 53 0.18
23 5 0.02
24 5 0.02
25 27 0.09
26 10 0.03
27 62 0.21
28 20 0.07
29 12 0.04
30 3 0.01
31 46 0.16
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (26 bp):
TATTAGATGGATTGATTTATTTTAAA
Found at i:24190 original size:20 final size:21
Alignment explanation
Indices: 24158--24197 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24148 TAATTTATAG
24158 TATGGATTGATTTATTTAAAA
1 TATGGATTGATTTATTTAAAA
*
24179 TATGGA-TGATTTTTTTAAA
1 TATGGATTGATTTATTTAAA
24198 TAATTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:24218 original size:79 final size:78
Alignment explanation
Indices: 24128--24366 Score: 285
Period size: 79 Copynumber: 3.1 Consensus size: 78
24118 TATTTTGTAG
*
24128 TTGTATAGATTTATTTTAAATAATTTATAGTATGGATTGATTTATTTAAAATATGGA-TGATTTT
1 TTGTATTGATTTATTTTAAATAATTTAT-GTATGGATTGATTTATTTAAAATATGGATTGATTTT
24192 TTTAAATAATTTTA
65 TTTAAATAATTTTA
* *
24206 GTTGTATTGATTTGTTTTAAAT-ATTTATTTGTATGGATTGATTTATTTTAAATATGGATTGA-T
1 -TTGTATTGATTTATTTTAAATAATTTA--TGTATGGATTGATTTATTTAAAATATGGATTGATT
* ** * *
24269 TTATTATGTAGTTGTA
63 TTTTTAAATAATTTTA
*
24285 -TGGATTGATTTATTTTAAATAATTTAT-TA--GATTGATTTATTTTAAAATATGGATTGATTTA
1 TTGTATTGATTTATTTTAAATAATTTATGTATGGATTGATTTA-TTTAAAATATGGATTGATTT-
24346 TTTTAAATAATTATTA
64 TTTTAAATAATT-TTA
24362 TTGTA
1 TTGTA
24367 GTTATATGAT
Statistics
Matches: 134, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
73 10 0.07
74 16 0.12
75 4 0.03
76 9 0.07
77 20 0.15
78 13 0.10
79 58 0.43
80 4 0.03
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (78 bp):
TTGTATTGATTTATTTTAAATAATTTATGTATGGATTGATTTATTTAAAATATGGATTGATTTTT
TTAAATAATTTTA
Found at i:24249 original size:31 final size:29
Alignment explanation
Indices: 24179--24260 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 29
24169 TTATTTAAAA
*
24179 TATGGA-TGATTTTTTTAAATAATTTTAG
1 TATGGATTGATTTTTTTAAATATTTTTAG
* *
24207 T-TGTATTGATTTGTTTTAAATATTTATTTG
1 TATGGATTGATTT-TTTTAAATATTT-TTAG
24237 TATGGATTGATTTATTTTAAATAT
1 TATGGATTGATTT-TTTTAAATAT
24261 GGATTGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.07
28 7 0.16
29 11 0.24
30 4 0.09
31 20 0.44
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.57
Consensus pattern (29 bp):
TATGGATTGATTTTTTTAAATATTTTTAG
Found at i:24286 original size:25 final size:22
Alignment explanation
Indices: 24229--24350 Score: 93
Period size: 25 Copynumber: 5.2 Consensus size: 22
24219 GTTTTAAATA
24229 TTTATTTGTATGGATTGATTTAT
1 TTTA-TTGTATGGATTGATTTAT
**
24252 TTTA-AATATGGATTGATTTAT
1 TTTATTGTATGGATTGATTTAT
24273 TATGTAGTTGTATGGATTGATTTAT
1 T-T-TA-TTGTATGGATTGATTTAT
* *
24298 TTTAAATAATTTATTAGATTGATTTAT
1 TTT--AT--TGTA-TGGATTGATTTAT
***
24325 TTTAAAATATGGATTGATTTAT
1 TTTATTGTATGGATTGATTTAT
24347 TTTA
1 TTTA
24351 AATAATTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 19
0.73 0.09 0.17
Matches are distributed among these distances:
21 16 0.20
22 17 0.21
23 9 0.11
24 2 0.03
25 18 0.22
26 3 0.04
27 15 0.19
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (22 bp):
TTTATTGTATGGATTGATTTAT
Found at i:24294 original size:177 final size:176
Alignment explanation
Indices: 23773--24354 Score: 475
Period size: 177 Copynumber: 3.2 Consensus size: 176
23763 TTTTAAAATA
*
23773 ATTTATTTTAAAATAATTTATTATAAAATGGATTGATTTATTTTAAATA-AT-TTATTTTAAATA
1 ATTTATTTT-AAATAATTTA-TAT---ATGGATTGATTTATTTTAAATATATATTTTTTTAAATA
* * * *
23836 ATTATTAGTATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTT-TTTAAAATATG
61 ATT-TTAGTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATATG
23900 AATTGATTTATTATTGTAGTTGTATTGATTGATTTATTTTAAATAATTTATTAGT
125 AATTGATTTATTA-TGTAGTTGTA-TGATTGATTTATTTT-AATAATTTATTAGT
** * ** * * * *
23955 ATGGA-TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATA-ATTATTAGTATTGATTGAT
1 ATTTATTTTAAATAATTT-ATATATGGATTGATTTATTTTAAATATA-TATT--T-TT--TTAAA
* * *
24018 TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTA-TTATATGGATTGATTTATTTTAAAT
59 TAATTTT--AGTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAT
* * * ** * * *
24082 ATTAGTATGGATTGATTTAT-T--TTAAAATAATTGATTTATTTT-GTAGTTGTA-TAG-
122 A-T-GAATTGATTTA-TTATGTAGTT-GTATGATTGATTTATTTTAATAATT-TATTAGT
*
24136 ATTTATTTTAAATAATTTATAGTATGGATTGATTTATTTAAAATATGGATGATTTTTTTAAATAA
1 ATTTATTTTAAATAATTTATA-TATGGATTGATTTATTTTAAATAT--AT-ATTTTTTTAAATAA
* * *
24201 TTTTAGT-TGTATTGATTTGTTTTAAAT-ATTTATTTGTATGGATTGATTTATTTTAAATATGGA
62 TTTTAGTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATATGAA
24264 TTGATTTATTATGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG-
127 TTGATTTATTATGTAGTTGTAT-GATTGATTTATTTT-AATAATTTATTAGT
* *
24315 ATTGA-TTT--AT--TTTAAAATATGGATTGATTTATTTTAAATA
1 ATTTATTTTAAATAATTT-ATATATGGATTGATTTATTTTAAATA
24355 ATTATTATTG
Statistics
Matches: 318, Mismatches: 51, Indels: 70
0.72 0.12 0.16
Matches are distributed among these distances:
174 29 0.09
175 11 0.03
176 10 0.03
177 81 0.25
178 8 0.03
179 13 0.04
180 17 0.05
181 8 0.03
182 44 0.14
183 5 0.02
184 38 0.12
185 40 0.13
186 2 0.01
187 9 0.03
188 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (176 bp):
ATTTATTTTAAATAATTTATATATGGATTGATTTATTTTAAATATATATTTTTTTAAATAATTTT
AGTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAATATGAATTGA
TTTATTATGTAGTTGTATGATTGATTTATTTTAATAATTTATTAGT
Found at i:24323 original size:27 final size:26
Alignment explanation
Indices: 24287--24361 Score: 104
Period size: 22 Copynumber: 3.0 Consensus size: 26
24277 TAGTTGTATG
24287 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTTAAATAA-TTATTA
*
24314 GATTGATTTATTTT-AA-AA-TA-TG
1 GATTGATTTATTTTAAATAATTATTA
24336 GATTGATTTATTTTAAATAATTATTA
1 GATTGATTTATTTTAAATAATTATTA
24362 TTGTAGTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 15 0.36
23 4 0.10
24 2 0.05
25 4 0.10
26 3 0.07
27 14 0.33
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (26 bp):
GATTGATTTATTTTAAATAATTATTA
Found at i:25512 original size:31 final size:31
Alignment explanation
Indices: 25477--25559 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
25467 TCATATAACA
25477 TTTACTTTTTGTTTCATTTTAGTACCCAGTG
1 TTTACTTTTTGTTTCATTTTAGTACCCAGTG
*
25508 TTTACTTTTTGTTTCATTTTAGT---CATTG
1 TTTACTTTTTGTTTCATTTTAGTACCCAGTG
*
25536 TTAAC-TTTT-TTTCATTTTAGTACC
1 TTTACTTTTTGTTTCATTTTAGTACC
25560 TAAATTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
26 12 0.26
27 4 0.09
28 8 0.17
31 23 0.49
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.59
Consensus pattern (31 bp):
TTTACTTTTTGTTTCATTTTAGTACCCAGTG
Found at i:25735 original size:30 final size:31
Alignment explanation
Indices: 25679--25745 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
25669 GTACTAAACA
*
25679 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGATCACTTTCGTTTTTATTTAAT
*
25710 TAAGATATGATCACTTTTG-TTTTATTTAAT
1 TAAGATATGATCACTTTCGTTTTTATTTAAT
25740 TAAGAT
1 TAAGAT
25746 GTGGTAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (31 bp):
TAAGATATGATCACTTTCGTTTTTATTTAAT
Found at i:27249 original size:244 final size:242
Alignment explanation
Indices: 26787--27276 Score: 921
Period size: 244 Copynumber: 2.0 Consensus size: 242
26777 AACTTACTAC
26787 AAATCACAAAAATTAATCAGCTCTACCATAACTAATCAATAACTACAAACAACAGCAGTAATCTA
1 AAATCACAAAAATTAATCAGCTCTACCATAACTAATCAATAACTACAAACAACAGCAGTAATCTA
26852 CTTCCCTCGTCTGCATTTTTTATTAGGTTGTGGGGTTGTTGTTTTGGATCGATTCTTTTGGTTAA
66 CTTCCCTCGTCTGCATTTTTTATTAGGTTGTGGGGTTGTTGTTTTGGATCGATTCTTTTGGTTAA
26917 GGGATGTCATCCATGCTCTCTACGTCAAATTGTTGATTTAAAACAGTGCGGGGGAAGGCTTGTGA
131 GGGATGTCATCCATGC-CTCTACGTCAAATTGTTGATTTAAAACAGTGCGGGGGAAGGCTTGTGA
26982 TGGTTAATGGAGGTTAACCCCTTCTAGTGTCAGAAAAGACTCGTTGGA
195 TGGTTAATGGAGGTTAACCCCTTCTAGTGTCAGAAAAGACTCGTTGGA
27030 AAATCACAAAAATTAATCAAGCTCTACCATAACTAATCAATAACTACACAAACAACAGCAGTAAT
1 AAATCACAAAAATTAATC-AGCTCTACCATAACTAATCAATAACT--ACAAACAACAGCAGTAAT
27095 CTACTT-CCTCGTCTGCATTTTTTATTAGGTTGTGGGGTTGTTGTTTTGGATCGATTCTTTTGGT
63 CTACTTCCCTCGTCTGCATTTTTTATTAGGTTGTGGGGTTGTTGTTTTGGATCGATTCTTTTGGT
27159 TAAGGGATGTCATCCATG-CTCTACGTCAAATTGTTGATTTAAAACAAGTGCGGGGGAAGGCTTG
128 TAAGGGATGTCATCCATGCCTCTACGTCAAATTGTTGATTTAAAAC-AGTGCGGGGGAAGGCTTG
27223 TGATGGTTAATGGAGGTTAACCCCTTCTAGTGTCAGAAAAGACTCGTTGGA
192 TGATGGTTAATGGAGGTTAACCCCTTCTAGTGTCAGAAAAGACTCGTTGGA
27274 AAA
1 AAA
27277 ATTTGGTGAT
Statistics
Matches: 243, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
243 45 0.19
244 98 0.40
245 76 0.31
246 24 0.10
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (242 bp):
AAATCACAAAAATTAATCAGCTCTACCATAACTAATCAATAACTACAAACAACAGCAGTAATCTA
CTTCCCTCGTCTGCATTTTTTATTAGGTTGTGGGGTTGTTGTTTTGGATCGATTCTTTTGGTTAA
GGGATGTCATCCATGCCTCTACGTCAAATTGTTGATTTAAAACAGTGCGGGGGAAGGCTTGTGAT
GGTTAATGGAGGTTAACCCCTTCTAGTGTCAGAAAAGACTCGTTGGA
Found at i:28637 original size:59 final size:59
Alignment explanation
Indices: 28511--28642 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 59
28501 TATGAATAGA
* * **
28511 CGAGTGACCATTTTATAACTTTTAATAATCGGAGGATTCAACAAAGCAACACCCTATAGT
1 CGAGGGACCATTTTATAACTTTTAATAATC-GAGGACTCAACAAAGCAACACCCTATAAC
* * * *
28571 CGAGGGACTATTTTATAACTTTTAATAAT-TATGGACTCAACAAAGTAATACCCTATAAC
1 CGAGGGACCATTTTATAACTTTTAATAATCGA-GGACTCAACAAAGCAACACCCTATAAC
28630 C-AGGGGACCATTT
1 CGA-GGGACCATTT
28643 GTGTACTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.03
59 32 0.52
60 27 0.44
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (59 bp):
CGAGGGACCATTTTATAACTTTTAATAATCGAGGACTCAACAAAGCAACACCCTATAAC
Found at i:34877 original size:18 final size:18
Alignment explanation
Indices: 34856--34890 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34846 CAAAGTTAAC
*
34856 GGGCATGTCAACGGTCAA
1 GGGCAGGTCAACGGTCAA
34874 GGGCAGGTCAACGGTCA
1 GGGCAGGTCAACGGTCA
34891 GGTCAAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.37, T:0.14
Consensus pattern (18 bp):
GGGCAGGTCAACGGTCAA
Found at i:36106 original size:31 final size:31
Alignment explanation
Indices: 36068--36139 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
36058 CCACTTTTTG
*
36068 AGATATGGTCACTTTCATTTTTATTTAATTA
1 AGATATGGTCACTTTCATTTTTATTTAAATA
* **
36099 AGATATGGTTACTTTTGTTTTTATTTAAATA
1 AGATATGGTCACTTTCATTTTTATTTAAATA
*
36130 A-ATGTGGTCA
1 AGATATGGTCA
36140 TCACAGGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (31 bp):
AGATATGGTCACTTTCATTTTTATTTAAATA
Found at i:36268 original size:27 final size:25
Alignment explanation
Indices: 36217--36270 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
36207 AACATAAAAT
**
36217 AAAATATTTTTAATAAGTTAATATA
1 AAAATATTTTTAATAAAATAATATA
*
36242 AAAATATTTTTTAAATAAAATATTATA
1 AAAATA-TTTTT-AATAAAATAATATA
36269 AA
1 AA
36271 CTTAAGCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATATTTTTAATAAAATAATATA
Found at i:39067 original size:4 final size:5
Alignment explanation
Indices: 38995--39069 Score: 53
Period size: 5 Copynumber: 13.8 Consensus size: 5
38985 GTTAAAAGAG
* * *
38995 AAAAT AAAAAT AAAAC AAAAC AAAAT AAAAT AAAAA AAGAAGT GGGAAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AA-T ---AAAAT
39046 AAAAAT AAAAT AAAAT -AAAT AAAA
1 -AAAAT AAAAT AAAAT AAAAT AAAA
39070 AAGTGTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.07
5 37 0.64
6 12 0.21
8 1 0.02
9 2 0.03
10 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:39087 original size:40 final size:39
Alignment explanation
Indices: 39041--39134 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 39
39031 AAGAAGTGGG
39041 AAAATAA-AAATAAAATAAAATAAATAAAAAAGTGTTAAAT
1 AAAATAATAAATAAAATAAAAT-AA-AAAAAAGTGTTAAAT
** *
39081 TTAATAATAGAACAAAATAAAATAAAAAAAAGTGTTAAAT
1 AAAATAATA-AATAAAATAAAATAAAAAAAAGTGTTAAAT
39121 AAAATAATAAATAA
1 AAAATAATAAATAA
39135 TAGCAGTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
39 4 0.09
40 27 0.59
41 3 0.07
42 12 0.26
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (39 bp):
AAAATAATAAATAAAATAAAATAAAAAAAAGTGTTAAAT
Found at i:39198 original size:18 final size:18
Alignment explanation
Indices: 39177--39219 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
39167 GTTATTTTTA
*
39177 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
39195 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
39213 AAATAAA
1 AAATAAA
39220 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:39736 original size:12 final size:12
Alignment explanation
Indices: 39715--39744 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39705 AGAAGTGTGC
39715 GAAAAATAGAGA
1 GAAAAATAGAGA
*
39727 GAAAACTAGAGA
1 GAAAAATAGAGA
39739 GAAAAA
1 GAAAAA
39745 AATAGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:40600 original size:156 final size:156
Alignment explanation
Indices: 40351--40667 Score: 449
Period size: 156 Copynumber: 2.0 Consensus size: 156
40341 GAAGGTTTTT
* * * * *
40351 GTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTCGGCTAGGAGATAGTTCCTTATT
1 GTTGACAGACAACCCTTCTCGCCTTGAGATATATTGTAAATTCGGCTAGGAGATAATTCATTATT
* *
40416 GCTAAATCGTAGCCAAACTAGGTATTCTTCTTGACTTAAAGACCTCAGTTT-AACTTTCAACCAG
66 GCTAAATCGTAGCCAAACTAAGTATTCTTCTTAACTTAAAGACCTCAGTTTAAAC-TTCAACCAG
*
40480 AAAGTAGTTCCTCGTTGGTACCATGCG
130 AAAGTAGTTCCTCGTTGCTACCATGCG
* * * *
40507 GTTGCCAGACAACCCTTCTTGCCTTGAGATATATTGTAAATTCGGCTGGGAGATAATTCATTGTT
1 GTTGACAGACAACCCTTCTCGCCTTGAGATATATTGTAAATTCGGCTAGGAGATAATTCATTATT
* * * * *
40572 GCTAAATGGTAGCC-AACATAAGTCTTCTTCTTAACTTAAAGTCTTCAGTTTAAACTTCAACTAG
66 GCTAAATCGTAGCCAAAC-TAAGTATTCTTCTTAACTTAAAGACCTCAGTTTAAACTTCAACCAG
40636 AAAGTAGTTCCTCGTTGCTACCATGCG
130 AAAGTAGTTCCTCGTTGCTACCATGCG
40663 GTTGA
1 GTTGA
40668 TATGCCTTCA
Statistics
Matches: 141, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
155 3 0.02
156 135 0.96
157 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (156 bp):
GTTGACAGACAACCCTTCTCGCCTTGAGATATATTGTAAATTCGGCTAGGAGATAATTCATTATT
GCTAAATCGTAGCCAAACTAAGTATTCTTCTTAACTTAAAGACCTCAGTTTAAACTTCAACCAGA
AAGTAGTTCCTCGTTGCTACCATGCG
Found at i:40867 original size:200 final size:200
Alignment explanation
Indices: 40512--40946 Score: 602
Period size: 200 Copynumber: 2.2 Consensus size: 200
40502 ATGCGGTTGC
* * * **
40512 CAGACAACCCTTCTTGCCTTGAGATATATTGTAAATTCGGCTGGGAGATAATTCATTGTTGCTAA
1 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAATTCATTGTTGCTAA
*** * *
40577 ATGGTAGCCAACATAAGTCTTCTTCTTAACTTAAAGTCTTCAGTTTAAACTTCAACTAGAAAGTA
66 ATCACAGCCAACATAAGTCTTCTTCTTAACTTAAAGTCCTCAGTTTAAACTTCAACCAGAAAGTA
*
40642 GTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCAAGCTGAATGGAATCGAACCCAAAAGTTTT
131 GTTCCTCGTTGCTACCATACGGTTGATATGCCTTCAAGCTGAATGGAATCGAACCCAAAAGTTTT
40707 GTTAA
196 GTTAA
* * *
40712 CAGATAACCCTTATCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAA
1 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAATTCATTGTTGCTAA
* * * * * *
40777 ATCACAGCCAACCTATGTCTTGTTCTTGACTTACA-TACCTCGGTTTAAACTTCAACCAGAAAGT
66 ATCACAGCCAACATAAGTCTTCTTCTTAACTTAAAGT-CCTCAGTTTAAACTTCAACCAGAAAGT
* * *
40841 AGTTCCTCGTTGCTACCATACGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAGTTT
130 AGTTCCTCGTTGCTACCATACGGTTGATATGCCTTCAAGCTGAATGGAATCGAACCCAAAAGTTT
*
40906 TGTTGA
195 TGTTAA
* * * *
40912 TATATATCTCTTCTCGCCTTGAGCTATGCTGTAAA
1 CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAA
40947 CGGTTCCTCT
Statistics
Matches: 205, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
199 1 0.00
200 204 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (200 bp):
CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTCGGCTGGGAGATAATTCATTGTTGCTAA
ATCACAGCCAACATAAGTCTTCTTCTTAACTTAAAGTCCTCAGTTTAAACTTCAACCAGAAAGTA
GTTCCTCGTTGCTACCATACGGTTGATATGCCTTCAAGCTGAATGGAATCGAACCCAAAAGTTTT
GTTAA
Found at i:41154 original size:86 final size:85
Alignment explanation
Indices: 41009--41305 Score: 398
Period size: 86 Copynumber: 3.5 Consensus size: 85
40999 ATTCTTTAGT
* * * * *
41009 TGACTCCCTTTCACGGGAAAGCCAAGTGGTATATTCTTCAAGTGGTTCCCTTTCGCAGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGGATATTCTTCAGGTGGTTCCCTTT-GCAGGTCTGAA
41074 CCAGGTGAGATGATCTTTGGA
65 CCAGGTGAGATGATCTTTGGA
* * *
41095 TGACTCCCCTTTACGGGAAAGGCATGTGGGATATTCTTCAGGTGGTTCCTCTTTACAGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGGATATTCTTCAGGTGGTTCC-CTTTGCAGGTCTGAA
41160 CCAGGTGAGATGATCTTTGGA
65 CCAGGTGAGATGATCTTTGGA
* * *
41181 TAACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGGATATTCTTCAGGTGGTT-CCCTTTGCAGGTCTGAA
* * *
41246 CCATGTGAGATTATCTTTAGA
65 CCAGGTGAGATGATCTTTGGA
* * *
41267 TGAC-CCTCCTTCACGAGAAAGTCATGTGAGATGTTCTTC
1 TGACTCC-CCTTCACGGGAAAGTCATGTGGGATATTCTTC
41306 GAGTGACTCC
Statistics
Matches: 187, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
85 2 0.01
86 179 0.96
87 6 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (85 bp):
TGACTCCCCTTCACGGGAAAGTCATGTGGGATATTCTTCAGGTGGTTCCCTTTGCAGGTCTGAAC
CAGGTGAGATGATCTTTGGA
Found at i:41319 original size:172 final size:172
Alignment explanation
Indices: 41011--41320 Score: 453
Period size: 172 Copynumber: 1.8 Consensus size: 172
41001 TCTTTAGTTG
* *
41011 ACTCCCTTTCACGGGAAAGCCAAGTGGTATATTCTTCAAGTGGTTCCCTTTCGCAGGTCTGAACC
1 ACTCCCCTTCACGGGAAAGCCAAGTGGTATATTCTTCAAGTGGTTCCCCTTCGCAGGTCTGAACC
* * * * **
41076 AGGTGAGATGATCTTTGGATGACTCCCCTTTACGGGAAAGGCATGTGGGATATTCTTCAGGTGGT
66 AGGTGAGATGATCTTTAGATGACTCCCCTTCACGAGAAAGGCATGTGAGATATTCTTCAGGTGAC
41141 TCCTCTTTACAGGTCTGAACCAGGTGAGATGATCTTTGGATA
131 TCCTCTTTACAGGTCTGAACCAGGTGAGATGATCTTTGGATA
* * *
41183 ACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCAGGTCTGAACC
1 ACTCCCCTTCACGGGAAAGCCAAGTGGTATATTCTTCAAGTGGTTCCCCTTCGCAGGTCTGAACC
* * * *
41248 ATGTGAGATTATCTTTAGATGAC-CCTCCTTCACGAGAAAGTCATGTGAGATGTTCTTC-GAGTG
66 AGGTGAGATGATCTTTAGATGACTCC-CCTTCACGAGAAAGGCATGTGAGATATTCTTCAG-GTG
41311 ACTCCTCTTT
129 ACTCCTCTTT
41321 GTGAGAAAGC
Statistics
Matches: 121, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
171 3 0.02
172 118 0.98
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (172 bp):
ACTCCCCTTCACGGGAAAGCCAAGTGGTATATTCTTCAAGTGGTTCCCCTTCGCAGGTCTGAACC
AGGTGAGATGATCTTTAGATGACTCCCCTTCACGAGAAAGGCATGTGAGATATTCTTCAGGTGAC
TCCTCTTTACAGGTCTGAACCAGGTGAGATGATCTTTGGATA
Found at i:45363 original size:33 final size:33
Alignment explanation
Indices: 45326--45392 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
45316 GACATTTTTC
45326 ACCTCTTGATAGTTATATAAAGCATGTAAAAGG
1 ACCTCTTGATAGTTATATAAAGCATGTAAAAGG
45359 ACCTCTTGATAGTTATATAAAGCATGTAAAAGG
1 ACCTCTTGATAGTTATATAAAGCATGTAAAAGG
45392 A
1 A
45393 TGGTGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (33 bp):
ACCTCTTGATAGTTATATAAAGCATGTAAAAGG
Found at i:52713 original size:3 final size:3
Alignment explanation
Indices: 52705--52742 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
52695 AATATATATT
52705 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
52743 TGGGTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53133 original size:114 final size:113
Alignment explanation
Indices: 52992--53881 Score: 1032
Period size: 114 Copynumber: 7.9 Consensus size: 113
52982 GCTTTTGATG
52992 AGTTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AGTTCTTCTCATTATGAACTTCT-TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* ** * * * *
53056 CTGAAAAAAATAACCCATCAAGTAATAGATTTGAGCAAAAAGGTTGAACA
65 CTGGAAAAGTTGATCCATCAAGTGAT-GATTTGAACAAAAAGGTTGAACA
* *
53106 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * *
53171 TGGCAAAA-ATAATCCATCAAGTGATGAATTCAGAC-AAAAGGTTGAACA
66 TGG-AAAAGTTGATCCATCAAGTGATGATTTGA-ACAAAAAGGTTGAACA
* *
53219 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTT
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTT
* * * *
53284 CTCTGGAAAAGATAATCCATTGAA-TGATGGATTTGAA-TAAAAGGTTGAACA
63 CTCTGGAAAAGTTGATCCA-TCAAGTGAT-GATTTGAACAAAAAGGTTGAACA
*
53335 AATTCTTCTCATTATGAACTTCTTCTT-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* *
53399 CTGGAAAAGTTGATCCAT--TGTTATGGATTTGAACAAAAA-GTTGAACA
65 CTGGAAAAGTTGATCCATCAAGTGAT-GATTTGAACAAAAAGGTTGAACA
*
53446 AGTTCTTCTCATTATGAACTTCTTCTTTCTTT-TTCAGATGAGTTCTTCTCATTATGAACTCTAC
1 AGTTCTTCTCATTATGAACTTCTTC-TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTC
* * * * ** *
53510 -CTGGCAATGTTGATTCATCAAATGATGAATTCAAACAAAAAAGTTGAACA
64 TCTGGAAAAGTTGATCCATCAAGTGATG-ATTTGAACAAAAAGGTTGAACA
53560 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCT
* * *
53624 C-GGAAATGTTGATCCAT--TGTTATGGATTTGAACAAAAA-GTTGAACA
65 CTGGAAAAGTTGATCCATCAAGTGAT-GATTTGAACAAAAAGGTTGAACA
* *
53670 AGTTCTTCTTATTATGAACTTCTTCTT-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACT-TTC
* * * ** *
53734 -CT-GACAATGTTGATTCATCAAATGATGAATTCAAACAAAAAAGTTGAACA
64 TCTGGA-AAAGTTGATCCATCAAGTGATG-ATTTGAACAAAAAGGTTGAACA
53784 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCT
* *
53848 C-GGAAATGTTGATCCATTGAA-TGATGGATTTGAA
65 CTGGAAAAGTTGATCCA-TCAAGTGAT-GATTTGAA
53882 TCTTTGCTAA
Statistics
Matches: 694, Mismatches: 49, Indels: 67
0.86 0.06 0.08
Matches are distributed among these distances:
109 1 0.00
110 71 0.10
111 113 0.16
112 14 0.02
113 166 0.24
114 219 0.32
115 10 0.01
116 92 0.13
117 8 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGTTGATCCATCAAGTGATGATTTGAACAAAAAGGTTGAACA
Found at i:53660 original size:224 final size:225
Alignment explanation
Indices: 52992--53881 Score: 1122
Period size: 224 Copynumber: 3.9 Consensus size: 225
52982 GCTTTTGATG
*
52992 AGTTCTTCTCATTATGAAC-T-TTCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC
1 AGTTCTTCTCATTATGAACTTCTTCT-TTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTAC
* * * * ** * *
53055 TCTGAAAAAAATAACCCATCAAGTAAT-AGATTTGAGCAAAAAGGTTGAACAAATTCTTCTCATT
64 TCTGAAAAAGATAATCCATCAAATGATGA-ATTCAAACAAAAAAGTTGAACAAATTCTTCTCATT
* ** *
53119 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAA-AATAA
128 ATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAATGTTGA
* * * *
53183 TCCATCAAGTGAT-GAATTCAGACAAAAGGTTGAACA
192 TCCAT--TGTGATGGATTTGA-ACAAAAAGTTGAACA
* * *
53219 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTT
1 AGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTA
* ** * ** * *
53284 CTCTGGAAAAGATAATCCATTGAATGATGGATTTGAA-TAAAAGGTTGAACAAATTCTTCTCATT
63 CTCTGAAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAAGTTGAACAAATTCTTCTCATT
*
53348 ATGAACTTCTTCTT-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGA
128 ATGAACTTCTTCTTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGA
*
53412 TCCATTGTTATGGATTTGAACAAAAAGTTGAACA
192 TCCATTGTGATGGATTTGAACAAAAAGTTGAACA
*
53446 AGTTCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACT
** * * * * *
53510 CTGGCAATGTTGATTCATCAAATGATGAATTCAAACAAAAAAGTTGAACAAGTTCTTCTCATTAT
65 CTGAAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAAGTTGAACAAATTCTTCTCATTAT
53575 GAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-C-GGAAATGTTGATC
130 GAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATC
*
53638 CATTGTTATGGATTTGAACAAAAAGTTGAACA
194 CATTGTGATGGATTTGAACAAAAAGTTGAACA
*
53670 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACT
* * * * * *
53734 CTGACAATGTTGATTCATCAAATGATGAATTCAAACAAAAAAGTTGAACAAGTTCTTCTCATTAT
65 CTGAAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAAGTTGAACAAATTCTTCTCATTAT
53799 GAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-C-GGAAATGTTGATC
130 GAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATC
53862 CATTGAATGATGGATTTGAA
194 CATTG--TGATGGATTTGAA
53882 TCTTTGCTAA
Statistics
Matches: 605, Mismatches: 43, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
224 284 0.47
225 72 0.12
226 16 0.03
227 82 0.14
228 11 0.02
229 90 0.15
230 50 0.08
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (225 bp):
AGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTC
TGAAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAAGTTGAACAAATTCTTCTCATTATG
AACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCA
TTGTGATGGATTTGAACAAAAAGTTGAACA
Found at i:54309 original size:22 final size:22
Alignment explanation
Indices: 54281--54335 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
54271 GATAAAGCTT
*
54281 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATATA
* * *
54303 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATATA
54325 TCATCTTTGAA
1 TCATCTTTGAA
54336 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:54779 original size:40 final size:40
Alignment explanation
Indices: 54723--54798 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
54713 TTTCAGCTTA
54723 GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
* *
54763 GATGTAAAACATTTGACAACACATTCATCTTTTTCT
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCT
54799 GTGGACTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
Found at i:59319 original size:11 final size:11
Alignment explanation
Indices: 59299--59328 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59289 CTTGATTCAA
*
59299 TTTTCCTTTTT
1 TTTTCTTTTTT
59310 TTTTCTTTTTT
1 TTTTCTTTTTT
59321 TTTTCTTT
1 TTTTCTTT
59329 CTTTGCTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:62616 original size:14 final size:14
Alignment explanation
Indices: 62582--62635 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
62572 TTGTGCAATA
* *
62582 CAAATGCAAAGATG
1 CAAATGTAAATATG
62596 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
62611 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
62625 TAAATGTAAAT
1 CAAATGTAAAT
62636 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:66408 original size:3 final size:3
Alignment explanation
Indices: 66400--66461 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
66390 AATATATATT
* * *
66400 TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66448 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
66462 TGGGTAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:72611 original size:21 final size:21
Alignment explanation
Indices: 72581--72622 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
72571 GTTGAAGTAT
72581 GTTGAAGATGCATGCTGGTAC
1 GTTGAAGATGCATGCTGGTAC
*
72602 GTTGAGGATGCATGCTGGTAC
1 GTTGAAGATGCATGCTGGTAC
72623 ACTCGTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (21 bp):
GTTGAAGATGCATGCTGGTAC
Found at i:74403 original size:23 final size:22
Alignment explanation
Indices: 74360--74403 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
74350 TCGAATAATA
* **
74360 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAAGATTTT
74382 TATTTAATAAAAATAGAGATTT
1 TATTTAATAAAAATA-AGATTT
74404 AATTGAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTTAATAAAAATAAGATTTT
Found at i:81253 original size:20 final size:20
Alignment explanation
Indices: 81228--81267 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
81218 CTAAACCCCA
81228 AATGAAAAAGGGTTATAAAG
1 AATGAAAAAGGGTTATAAAG
81248 AATGAAAAAGGGTTATAAAG
1 AATGAAAAAGGGTTATAAAG
81268 TATTCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (20 bp):
AATGAAAAAGGGTTATAAAG
Found at i:83245 original size:20 final size:20
Alignment explanation
Indices: 83220--83259 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
83210 GGTAGGGCAC
*
83220 ACCAACTACAATGAGCATTT
1 ACCAACTACAATGAACATTT
83240 ACCAACTACAATGAACATTT
1 ACCAACTACAATGAACATTT
83260 GAACCTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (20 bp):
ACCAACTACAATGAACATTT
Found at i:86514 original size:4 final size:4
Alignment explanation
Indices: 86507--86533 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
86497 TGAATGAATA
86507 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
86534 ATTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:86537 original size:3 final size:3
Alignment explanation
Indices: 86529--86573 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
86519 ATTTATTTAT
86529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
86574 TTTAGTATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:91608 original size:13 final size:13
Alignment explanation
Indices: 91590--91632 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
91580 AGATAAATAA
91590 CATATAAAAAAAT
1 CATATAAAAAAAT
91603 CATATATAAAAACAT
1 CATATA-AAAAA-AT
* *
91618 CATTTAAATAAAT
1 CATATAAAAAAAT
91631 CA
1 CA
91633 GCATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 10 0.38
14 9 0.35
15 7 0.27
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (13 bp):
CATATAAAAAAAT
Found at i:91609 original size:15 final size:15
Alignment explanation
Indices: 91591--91632 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
91581 GATAAATAAC
91591 ATATAAAAAAATCAT
1 ATATAAAAAAATCAT
*
91606 ATATAAAAACATCAT
1 ATATAAAAAAATCAT
*
91621 -T-TAAATAAATCA
1 ATATAAAAAAATCA
91633 GCATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 14 0.58
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATAAAAAAATCAT
Found at i:93416 original size:17 final size:18
Alignment explanation
Indices: 93394--93434 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
93384 TTACTTAAAA
*
93394 AAATTGATTAAAAATTC-
1 AAATTGATCAAAAATTCT
*
93411 AAATTGATCCAAAATTCT
1 AAATTGATCAAAAATTCT
93429 AAATTG
1 AAATTG
93435 CCCTTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (18 bp):
AAATTGATCAAAAATTCT
Found at i:98206 original size:18 final size:19
Alignment explanation
Indices: 98183--98222 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
98173 AACCCAGAAT
98183 TTCCATTTTAAGCAC-AAA
1 TTCCATTTTAAGCACGAAA
98201 TTCCATTTTAAGCACGAAA
1 TTCCATTTTAAGCACGAAA
98220 TTC
1 TTC
98223 ACTCTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (19 bp):
TTCCATTTTAAGCACGAAA
Done.