Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007086.1 Hibiscus syriacus cultivar Beakdansim tig00018485_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: 79134
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4490 original size:4 final size:4
Alignment explanation
Indices: 4483--4515 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
4473 AAAATAAATA
4483 AAAG AAAG AAA- AAAG AAAG AAA- AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
4516 AAAATAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4496 original size:11 final size:11
Alignment explanation
Indices: 4482--4518 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
4472 AAAAATAAAT
4482 AAAAGAAAGAA
1 AAAAGAAAGAA
4493 AAAAGAAAGAA
1 AAAAGAAAGAA
4504 AAAAGAAAGAA
1 AAAAGAAAGAA
4515 AAAA
1 AAAA
4519 ATAAGTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:4499 original size:7 final size:8
Alignment explanation
Indices: 4483--4515 Score: 52
Period size: 7 Copynumber: 4.4 Consensus size: 8
4473 AAAATAAATA
4483 AAAGAAAG
1 AAAGAAAG
4491 AAA-AAAG
1 AAAGAAAG
4498 AAAGAAA-
1 AAAGAAAG
4505 AAAGAAAG
1 AAAGAAAG
4513 AAA
1 AAA
4516 AAAATAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.61
8 9 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAGAAAG
Found at i:5623 original size:12 final size:11
Alignment explanation
Indices: 5599--5628 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5589 AAAAATAGAA
5599 AATAATATAAT
1 AATAATATAAT
5610 AATAATATTAAT
1 AATAATA-TAAT
5622 AATAATA
1 AATAATA
5629 AATTAAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAATATAAT
Found at i:5680 original size:17 final size:17
Alignment explanation
Indices: 5660--5710 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5650 AGTTTTTTAA
5660 AATAAAAATAAAAAATT
1 AATAAAAATAAAAAATT
5677 AATAAAAGA-AAAAAA-T
1 AATAAAA-ATAAAAAATT
* *
5693 AAT-TAAATAACAAATT
1 AATAAAAATAAAAAATT
5709 AA
1 AA
5711 ATAGATTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 7 0.24
17 13 0.45
18 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AATAAAAATAAAAAATT
Found at i:5683 original size:16 final size:16
Alignment explanation
Indices: 5664--5710 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
5654 TTTTAAAATA
5664 AAAATAAAAAATTAAT
1 AAAATAAAAAATTAAT
* *
5680 AAAAGAAAAAAATAAT
1 AAAATAAAAAATTAAT
* *
5696 TAAATAACAAATTAA
1 AAAATAAAAAATTAA
5711 ATAGATTGAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAATAAAAAATTAAT
Found at i:6364 original size:63 final size:64
Alignment explanation
Indices: 6263--6413 Score: 184
Period size: 63 Copynumber: 2.4 Consensus size: 64
6253 TATAGCATTT
* *
6263 AAATTCCTAAAAATAAGCTAAAACATCTTAAATCCTAATTAAAACACTTAAAAC-TATTTAAACT
1 AAATACCTAAAAATAAGATAAAACATCTTAAATCCTAATT-AAACAC-TAAAACTTATTTAAACT
6327 A
64 A
* * *
6328 AAATACCTAAAAATAATATAATA-ATC-TAAATCCTAATTAAATACTAAAACTTATTTAAACTA
1 AAATACCTAAAAATAAGATAAAACATCTTAAATCCTAATTAAACACTAAAACTTATTTAAACTA
*
6390 AAAGTACCTATAACA-AAGATAAAA
1 AAA-TACCTA-AAAATAAGATAAAA
6414 TATAAAATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
61 6 0.08
62 19 0.25
63 25 0.33
64 6 0.08
65 19 0.25
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (64 bp):
AAATACCTAAAAATAAGATAAAACATCTTAAATCCTAATTAAACACTAAAACTTATTTAAACTA
Found at i:8144 original size:12 final size:12
Alignment explanation
Indices: 8129--8153 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8119 GAAAAAAAAT
8129 AAAATAAAATAA
1 AAAATAAAATAA
8141 AAAATAAAATAA
1 AAAATAAAATAA
8153 A
1 A
8154 TGGAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:8166 original size:14 final size:15
Alignment explanation
Indices: 8119--8182 Score: 66
Period size: 14 Copynumber: 4.6 Consensus size: 15
8109 TCTGTTCAAA
*
8119 GAAAAAAAATAAAAT
1 GAAAATAAATAAAAT
8134 -AAAAT-AA-AAAAT
1 GAAAATAAATAAAAT
**
8146 -AAAATAAATGGAAT
1 GAAAATAAATAAAAT
8160 G-AAATAAATAAAAT
1 GAAAATAAATAAAAT
8174 GAAAATAAA
1 GAAAATAAA
8183 ACAAAATGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 10 0.25
13 4 0.10
14 19 0.47
15 7 0.17
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (15 bp):
GAAAATAAATAAAAT
Found at i:8168 original size:4 final size:5
Alignment explanation
Indices: 8120--8189 Score: 56
Period size: 5 Copynumber: 14.0 Consensus size: 5
8110 CTGTTCAAAG
** *
8120 AAAA- AAAAT AAAAT AAAAT AAAAAAT AAAAT -AAAT GGAAT GAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
8169 AAAAT GAAAAT AAAAC AAAAT
1 AAAAT -AAAAT AAAAT AAAAT
8190 GGGTTACCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
4 12 0.21
5 34 0.61
6 5 0.09
7 5 0.09
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:11091 original size:19 final size:19
Alignment explanation
Indices: 11069--11113 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
11059 GTTGTTTTTA
11069 AAATAAAA-ATAAAAAAATT
1 AAATAAAAGA-AAAAAAATT
*
11088 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAAAAATT
11107 AAATAAA
1 AAATAAA
11114 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAAAAGAAAAAAAATT
Found at i:13754 original size:40 final size:40
Alignment explanation
Indices: 13699--13820 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
13689 TGCAGGTTTA
*
13699 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
13739 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
13779 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
13819 TA
1 TA
13821 GCACTACGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:14079 original size:48 final size:48
Alignment explanation
Indices: 13925--14092 Score: 182
Period size: 54 Copynumber: 3.5 Consensus size: 48
13915 ATAAGCATAC
* * *
13925 AAATAAGCTTACGAGCTTTTGGAA--T-AATGGCAAGTATATGGGT-A
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGTAA
*
13969 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGAAAAAAATAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTG------GTAA
* * *
14023 TAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGTAA
*
14071 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
14093 GATGAAAGGT
Statistics
Matches: 105, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
44 23 0.22
46 1 0.01
47 14 0.13
48 24 0.23
53 1 0.01
54 42 0.40
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (48 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGTAA
Found at i:15095 original size:65 final size:65
Alignment explanation
Indices: 14968--15095 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
14958 TAAAACATCT
*
14968 TAAATCCTAATTAAAATACTTAAAACTATTTAAACAAAAATACCTAAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACAAAAATACCTAAAAAAATAATAAAATATTC
* *
15033 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAA-GATAAAATAT
1 TAAATCCTAATTAAAATACTTAAAA-CTATTTAAACAAAAATACCTAAAA-AAATAATAAAATAT
15096 AAAAATAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 5 0.09
65 50 0.86
66 3 0.05
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (65 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAACAAAAATACCTAAAAAAATAATAAAATATTC
Found at i:18189 original size:15 final size:15
Alignment explanation
Indices: 18163--18196 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18153 TATTAAAATT
18163 AAAATAAAAAATAAA
1 AAAATAAAAAATAAA
18178 GAAAAT-AAAAATAAA
1 -AAAATAAAAAATAAA
18193 AAAA
1 AAAA
18197 CTAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 9 0.50
16 5 0.28
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAATAAA
Found at i:24472 original size:29 final size:29
Alignment explanation
Indices: 24438--24510 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
24428 AAAGAATCAA
*
24438 AATTAAAGGCGTAAAGAGAATAACAAAAT
1 AATTAAAAGCGTAAAGAGAATAACAAAAT
24467 AATTAAAAGCGTAAAGAGAATAACAAAAT
1 AATTAAAAGCGTAAAGAGAATAACAAAAT
*
24496 AATTAAAAGCATAAA
1 AATTAAAAGCGTAAA
24511 TATAAATCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.18
Consensus pattern (29 bp):
AATTAAAAGCGTAAAGAGAATAACAAAAT
Found at i:24800 original size:20 final size:20
Alignment explanation
Indices: 24775--24883 Score: 60
Period size: 20 Copynumber: 5.2 Consensus size: 20
24765 AATTGATTTG
24775 AAAATAATATATATAATATA
1 AAAATAATATATATAATATA
* **
24795 AAAAT-ATTTATAATGGTATA
1 AAAATAATATAT-ATAATATA
* * *
24815 AAAA-AGTACATGCATTATATA
1 AAAATAATATAT--ATAATATA
* *
24836 AACATAATATAGATAATATTA
1 AAAATAATATATATAATA-TA
*
24857 ACAATATAAAAATATATAATATA
1 A-AA-AT-AATATATATAATATA
24880 AAAA
1 AAAA
24884 GATAAAAAAA
Statistics
Matches: 64, Mismatches: 17, Indels: 15
0.67 0.18 0.16
Matches are distributed among these distances:
19 5 0.08
20 23 0.36
21 13 0.20
22 7 0.11
23 5 0.08
24 11 0.17
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATAATATATATAATATA
Found at i:25230 original size:14 final size:13
Alignment explanation
Indices: 25210--25253 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
25200 ATAATAAAAC
25210 AAAATAAAATATA
1 AAAATAAAATATA
*
25223 AGAAATAAAAGATA
1 A-AAATAAAATATA
25237 AAAGATAAAATA-A
1 AAA-ATAAAATATA
25250 AAAA
1 AAAA
25254 GAATTACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.04
13 7 0.26
14 19 0.70
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (13 bp):
AAAATAAAATATA
Found at i:25253 original size:21 final size:22
Alignment explanation
Indices: 25202--25255 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
25192 CGGCGATCAT
* *
25202 AATAAAACAAAATAAAATATAAG
1 AATAAAA-AAGATAAAAGATAAG
*
25225 AA-ATAAAAGATAAAAGATAA-
1 AATAAAAAAGATAAAAGATAAG
25245 AATAAAAAAGA
1 AATAAAAAAGA
25256 ATTACCTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 3 0.12
23 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
AATAAAAAAGATAAAAGATAAG
Found at i:25287 original size:152 final size:153
Alignment explanation
Indices: 25042--25320 Score: 452
Period size: 152 Copynumber: 1.8 Consensus size: 153
25032 AAGTCGATAT
* * **
25042 CGATTATAATAAAACAAAACAAAATATATGAAATAAAAGATAAAAAGATAAAATAAAAAAGTGCT
1 CGATCATAATAAAACAAAACAAAATATAAGAAATAAAAGATAAAAAGATAAAATAAAAAAGAACT
*
25107 ACCTTTAAGGGTCTGTTTGTTTCACTGTAATTGGTTTTCCAGAAAATGCTTTCAACATTTTCTAC
66 ACCTTTAAGGGTCTGTTTGTTTCACTGTAATTGATTTTCCAGAAAATGCTTTCAACATTTTCTAC
25172 ATTTTTCAGTGTTTGGTTGACGG
131 ATTTTTCAGTGTTTGGTTGACGG
* *
25195 CGATCATAATAAAACAAAATAAAATATAAGAAATAAAAGAT-AAAAGATAAAATAAAAAAGAATT
1 CGATCATAATAAAACAAAACAAAATATAAGAAATAAAAGATAAAAAGATAAAATAAAAAAGAACT
* * * *
25259 ACCTTTAAGGGTTTGTTTGTTTCCCTGTAATTGATTTTCCAGAAAATGTTTTCCACATTTTC
66 ACCTTTAAGGGTCTGTTTGTTTCACTGTAATTGATTTTCCAGAAAATGCTTTCAACATTTTC
25321 CAGTGTTTGG
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
152 77 0.67
153 38 0.33
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (153 bp):
CGATCATAATAAAACAAAACAAAATATAAGAAATAAAAGATAAAAAGATAAAATAAAAAAGAACT
ACCTTTAAGGGTCTGTTTGTTTCACTGTAATTGATTTTCCAGAAAATGCTTTCAACATTTTCTAC
ATTTTTCAGTGTTTGGTTGACGG
Found at i:25528 original size:28 final size:28
Alignment explanation
Indices: 25475--25535 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
25465 CTCAAAACAT
*
25475 TATTATTTTATATATTTAAAATTAAATA
1 TATTATTTTATATATTTAAAATTAAAAA
*
25503 TATTATTTTATTATCATTT-TAA-TAAAAA
1 TATTATTTTA-TAT-ATTTAAAATTAAAAA
25531 TATTA
1 TATTA
25536 ATTGTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 20 0.69
29 5 0.17
30 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TATTATTTTATATATTTAAAATTAAAAA
Found at i:25804 original size:42 final size:40
Alignment explanation
Indices: 25743--25839 Score: 97
Period size: 42 Copynumber: 2.4 Consensus size: 40
25733 TAATAGTTTA
* ** * * *
25743 ATAATATTATTATCCTAATAAGTAATTAATATACTTAATAAT
1 ATAATATTTTTATTTTAATAAATAATTAATA-AATAAAT-AT
*
25785 ATAATATTTTTATTTTAATAAATATTTAATAAATAAATAT
1 ATAATATTTTTATTTTAATAAATAATTAATAAATAAATAT
25825 A-ATATATTTTTATTT
1 ATA-ATATTTTTATTT
25840 GATAAAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.02
40 15 0.32
41 5 0.11
42 26 0.55
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (40 bp):
ATAATATTTTTATTTTAATAAATAATTAATAAATAAATAT
Found at i:25828 original size:24 final size:25
Alignment explanation
Indices: 25800--25862 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
25790 ATTTTTATTT
25800 TAATAAATATTTAATAAAT-AAATA
1 TAATAAATATTTAATAAATAAAATA
* * * **
25824 TAATATATTTTTATTTGATAAAATA
1 TAATAAATATTTAATAAATAAAATA
25849 TAAT-AATA-TTAATA
1 TAATAAATATTTAATA
25863 GTTTTATTGA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
23 4 0.14
24 16 0.55
25 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATAAATATTTAATAAATAAAATA
Found at i:25928 original size:14 final size:14
Alignment explanation
Indices: 25882--25921 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
25872 AAAATTGTAG
25882 ATATAATATT-TTA
1 ATATAATATTATTA
25895 ATAATAATATTA-TA
1 AT-ATAATATTATTA
25909 ATA-AATATTATTA
1 ATATAATATTATTA
25922 GATAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 7 0.29
13 5 0.21
14 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATAATATTATTA
Found at i:26103 original size:14 final size:14
Alignment explanation
Indices: 26069--26103 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
26059 CAAACACTGT
*
26069 AAAATGATTTCCAG
1 AAAATGTTTTCCAG
*
26083 AAAATGTTTTCTAG
1 AAAATGTTTTCCAG
26097 AAAATGT
1 AAAATGT
26104 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (14 bp):
AAAATGTTTTCCAG
Found at i:27271 original size:26 final size:26
Alignment explanation
Indices: 27227--27282 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
27217 TTACTCGATG
* * *
27227 AGTTCATCTATAAATTGAATAGTAAA
1 AGTTCATCTATAAACTGAAAAATAAA
*
27253 AGTTCATCTATAAGCTGAAAAATAAA
1 AGTTCATCTATAAACTGAAAAATAAA
27279 AGTT
1 AGTT
27283 AATAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (26 bp):
AGTTCATCTATAAACTGAAAAATAAA
Found at i:28745 original size:3 final size:3
Alignment explanation
Indices: 28739--28766 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28729 AAAAAAAAAT
28739 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28767 ATTAACTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28898 original size:13 final size:13
Alignment explanation
Indices: 28873--28914 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
28863 TAAATAAGTA
28873 AAAAAACAA-AAT
1 AAAAAACAATAAT
*
28885 AAACAAA-AGTAAT
1 AAA-AAACAATAAT
28898 AAAAAACAATAAT
1 AAAAAACAATAAT
28911 AAAA
1 AAAA
28915 TAAATTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAAACAATAAT
Found at i:29027 original size:18 final size:17
Alignment explanation
Indices: 29004--29045 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
28994 AACAACATGA
29004 AGAAAAAGA-ATTGAAAAT
1 AGAAAAA-ATATT-AAAAT
*
29022 ATAAAAAATATTAAAAT
1 AGAAAAAATATTAAAAT
29039 AGAAAAA
1 AGAAAAA
29046 CTAAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (17 bp):
AGAAAAAATATTAAAAT
Found at i:30235 original size:3 final size:3
Alignment explanation
Indices: 30227--30286 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
30217 TTAAATAAGA
* * *
30227 AAT AAT AAT AAT AAAT AA- AAT AAT TAC ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30272 AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
30287 GTATAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30247 original size:33 final size:33
Alignment explanation
Indices: 30210--30281 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
30200 ACATAAAACA
*
30210 AAAATGATTA-AATAAGAAATAATAATAATAAAT
1 AAAATAATTACAATAA-AAATAATAATAATAAAT
* *
30243 AAAATAATTACACTAATAATAATAATAAT-AAT
1 AAAATAATTACAATAAAAATAATAATAATAAAT
30275 AATAATA
1 AA-AATA
30282 TAATAGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 5 0.15
33 25 0.74
34 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAATAATTACAATAAAAATAATAATAATAAAT
Found at i:30303 original size:8 final size:7
Alignment explanation
Indices: 30256--30303 Score: 50
Period size: 6 Copynumber: 7.1 Consensus size: 7
30246 ATAATTACAC
30256 TAATA-A
1 TAATATA
30262 TAATA-A
1 TAATATA
30268 TAATA-A
1 TAATATA
30274 TAATAATA
1 TAAT-ATA
30282 TAATAGTA
1 TAATA-TA
30290 TAATATA
1 TAATATA
30297 T-ATATA
1 TAATATA
30303 T
1 T
30304 TTTTTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 22 0.56
7 5 0.13
8 12 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (7 bp):
TAATATA
Found at i:30432 original size:11 final size:11
Alignment explanation
Indices: 30416--30440 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30406 TATATAATAT
30416 AAATGTTTTCA
1 AAATGTTTTCA
30427 AAATGTTTTCA
1 AAATGTTTTCA
30438 AAA
1 AAA
30441 CTATATATCA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:30461 original size:36 final size:36
Alignment explanation
Indices: 30396--30526 Score: 119
Period size: 36 Copynumber: 3.6 Consensus size: 36
30386 ATATATACAT
*
30396 TTTTAAAAACTATATA-ATATAAATGTTTTCAAAATG-
1 TTTTCAAAACTATATATATATAAA--TTTTCAAAATGC
* *
30432 TTTTCAAAACTATATATCATATAAATTTTCAAAAAAGGT
1 TTTTCAAAACTATATAT-ATATAAATTTTC--AAAATGC
** *
30471 TTTTCAAAACTATAT-TATATACGTTTTAAAAATGC
1 TTTTCAAAACTATATATATATAAATTTTCAAAATGC
30506 TTTT-AAATA-TATATATATATA
1 TTTTCAAA-ACTATATATATATA
30527 TATATATATA
Statistics
Matches: 81, Mismatches: 7, Indels: 15
0.79 0.07 0.15
Matches are distributed among these distances:
34 8 0.10
35 16 0.20
36 20 0.25
37 9 0.11
38 13 0.16
39 15 0.19
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (36 bp):
TTTTCAAAACTATATATATATAAATTTTCAAAATGC
Found at i:30519 original size:2 final size:2
Alignment explanation
Indices: 30512--30554 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30502 ATGCTTTTAA
30512 AT AT AT AT AT AT AT 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 AT AT AT AT
30554 A
1 A
30555 CATTTCCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30571 original size:98 final size:96
Alignment explanation
Indices: 30464--30642 Score: 213
Period size: 98 Copynumber: 1.8 Consensus size: 96
30454 AAATTTTCAA
* * *
30464 AAAAGGTTTTTCAAA-AC-TATATTATATACGTTTTAAAAATGCTTTT-AAATATATATATATAT
1 AAAAGG-TTTTCAAAGACATATATTATATA--TTTTAAAAATG-TTTTCAAAAAAACATATAT-T
30526 ATATAT-ATATATATATATATATATATATACATTTCC
61 ATATATCATATA-ATATATATATATATATACATTTCC
* *
30562 AAAATGTTTTCAAAGACTATATATTATATATTTTTAAAATGTTTTCGAAAAAAACATATATTATA
1 AAAAGGTTTTCAAAGAC-ATATATTATATATTTTAAAAATGTTTTC-AAAAAAACATATATTATA
30627 TATCATATAATATATA
64 TATCATATAATATATA
30643 CTTTTCAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
97 12 0.17
98 31 0.44
99 16 0.23
100 11 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (96 bp):
AAAAGGTTTTCAAAGACATATATTATATATTTTAAAAATGTTTTCAAAAAAACATATATTATATA
TCATATAATATATATATATATATACATTTCC
Found at i:30603 original size:35 final size:36
Alignment explanation
Indices: 30543--30629 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
30533 TATATATATA
* *
30543 TATATATATATACATTTCCAAAATGTTTTC-AAAGAC
1 TATATAT-TATATATTTCCAAAATGTTTTCAAAAAAC
**
30579 TATATATTATATATTTTTAAAATGTTTTCGAAAAAAAC
1 TATATATTATATATTTCCAAAATGTTTTC--AAAAAAC
30617 -ATATATTATATAT
1 TATATATTATATAT
30630 CATATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
35 19 0.43
36 7 0.16
37 13 0.30
38 5 0.11
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (36 bp):
TATATATTATATATTTCCAAAATGTTTTCAAAAAAC
Found at i:31434 original size:81 final size:81
Alignment explanation
Indices: 31275--32132 Score: 922
Period size: 81 Copynumber: 10.4 Consensus size: 81
31265 TTATTGACAA
* * * * * * * * * *
31275 ATAACCCTTCTTGTCTTGAGCTATGTTGTAAACGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACT
** *
31340 CGGGGGTC-CTTGGCAG
65 CGAAGGTCTTTTGGCAG
* *
31356 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
31421 GAAGGTCTTTTGGCGACAG
66 GAAGGTCTTTT-G-G-CAG
* * * * *
31440 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACT
* ** *
31505 TGGGGGTC-CTTGGCAG
65 CGAAGGTCTTTTGGCAG
* * *
31521 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
*
31586 AAAGGTCTTTTGTTAGCAG
66 GAAGGTCTTTTG---GCAG
* * * *
31605 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGT-GATCGAAC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAG-TCGAAC
**
31669 TCGGGGGTC-TTTGGCAG
64 TCGAAGGTCTTTTGGCAG
* *
31686 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
31751 GAAGGTCTTTTGGTCACAG
66 GAAGGTCTTTTGG---CAG
* * * * * * * *
31770 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACT
**
31835 CGGGGGTC-TTTGGCAG
65 CGAAGGTCTTTTGGCAG
* * *
31851 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
31916 -AAGGTCTTTTGTTAGCAG
66 GAAGGTCTTTTG---GCAG
* * * *
31934 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGT-GATCGAAC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAG-TCGAAC
**
31998 TCGGGGGTC-TTTGGCAG
64 TCGAAGGTCTTTTGGCAG
*
32015 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTCGAAGCTGAGCGTAGTCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAAGCTGAGCGTAGTCGAACT
*
32080 CAAAGGTCTTTTGTTAGCAG
65 CGAAGGTCTTTTG---GCAG
* *
32100 ATAACCCTTCTTGACTTAAGTTATACTGCAAAT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAAT
32133 AGTTTGTTAA
Statistics
Matches: 646, Mismatches: 101, Indels: 56
0.80 0.13 0.07
Matches are distributed among these distances:
79 4 0.01
80 106 0.16
81 220 0.34
82 7 0.01
83 42 0.07
84 151 0.23
85 116 0.18
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (81 bp):
ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTTGGCAG
Found at i:31547 original size:165 final size:165
Alignment explanation
Indices: 31315--32132 Score: 1417
Period size: 165 Copynumber: 5.0 Consensus size: 165
31305 AACGATATGA
* *
31315 CCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
* **
31380 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG-GCGACAGATAA
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAG-CAGATAA
31444 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
130 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
* * *
31480 CCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
31545 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
31610 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
131 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
*
31645 CCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
* *
31710 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCA-CAGATAA
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-GTTAGCAGATAA
* * * * *
31774 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
130 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
*
31810 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
31875 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAGGTCTTTTGTTAGCAGATAAC
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
31939 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
131 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
*
31974 CCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
*
32039 GCTGCAAATGATGTGCCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAA
66 GCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAA
32104 CCCTTCTTGACTTAAGTTATACTGCAAAT
130 CCCTTCTTGACTTAAGTTATACTGCAAAT
32133 AGTTTGTTAA
Statistics
Matches: 620, Mismatches: 28, Indels: 9
0.94 0.04 0.01
Matches are distributed among these distances:
163 3 0.00
164 130 0.21
165 432 0.70
166 55 0.09
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
Found at i:35515 original size:18 final size:19
Alignment explanation
Indices: 35474--35518 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
35464 AGTTAATATG
35474 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
35493 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
35511 AATGCAAA
1 AATGCAAA
35519 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:37225 original size:3 final size:3
Alignment explanation
Indices: 37219--37249 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
37209 AAAAAAAAAT
37219 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
37250 ATTAACTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:37382 original size:13 final size:13
Alignment explanation
Indices: 37357--37398 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
37347 TAAATAAGTA
37357 AAAAAACAA-AAT
1 AAAAAACAATAAT
*
37369 AAACAAA-AGTAAT
1 AAA-AAACAATAAT
37382 AAAAAACAATAAT
1 AAAAAACAATAAT
37395 AAAA
1 AAAA
37399 TAAATTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAAACAATAAT
Found at i:38723 original size:3 final size:3
Alignment explanation
Indices: 38715--38780 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
38705 TTAAATAAGA
* * *
38715 AAT AAT AAT AAT AAAT AAAT AAT TAC ACT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
38763 AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT A
38781 GTATAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.78
4 10 0.19
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38765 original size:19 final size:20
Alignment explanation
Indices: 38715--38799 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 20
38705 TTAAATAAGA
38715 AATA-ATAATAATAAATAAAT
1 AATACATAATAAT-AATAAAT
38735 AATTACACTAATAATAAT-AAT
1 AA-TACA-TAATAATAATAAAT
*
38756 AATAAATAATAATAATAATAT
1 AATACATAATAATAATAA-AT
*
38777 AATAGTATAATATATATATAAAT
1 AATA-CATAATA-ATA-ATAAAT
38800 TTTTTAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
19 10 0.18
20 6 0.11
21 13 0.24
22 10 0.18
23 12 0.22
24 4 0.07
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (20 bp):
AATACATAATAATAATAAAT
Found at i:38786 original size:13 final size:14
Alignment explanation
Indices: 38716--38790 Score: 75
Period size: 13 Copynumber: 5.2 Consensus size: 14
38706 TAAATAAGAA
38716 ATAATAATAATAA-
1 ATAATAATAATAAT
38729 ATAAATAATTACACTAAT
1 AT-AATAA-TA-A-TAAT
38747 AATAATAATAATAA-
1 -ATAATAATAATAAT
38761 ATAATAATAATAAT
1 ATAATAATAATAAT
*
38775 ATAATAGT-ATAAT
1 ATAATAATAATAAT
38788 ATA
1 ATA
38791 TATATAAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
13 23 0.43
14 12 0.22
15 5 0.09
16 2 0.04
17 5 0.09
18 5 0.09
19 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:38929 original size:11 final size:11
Alignment explanation
Indices: 38913--38937 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38903 TATATAATAT
38913 AAATGTTTTCA
1 AAATGTTTTCA
38924 AAATGTTTTCA
1 AAATGTTTTCA
38935 AAA
1 AAA
38938 CTATATCATA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:38979 original size:37 final size:36
Alignment explanation
Indices: 38892--38986 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
38882 TATATATACA
* *
38892 TTTTTAAAAACTATATAATATAAATGTTTTCAAAATG
1 TTTTTCAAAACTATATAATATAAA-GTTTTCAAAAGG
*
38929 -TTTTCAAAACTATATCATATAAA-TTTTCAAAAAAGG
1 TTTTTCAAAACTATATAATATAAAGTTTTC--AAAAGG
*
38965 TTTTTCAAAACTATATATTATA
1 TTTTTCAAAACTATATAATATA
38987 CGTTTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 5 0.10
36 26 0.52
37 19 0.38
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
TTTTTCAAAACTATATAATATAAAGTTTTCAAAAGG
Found at i:39013 original size:2 final size:2
Alignment explanation
Indices: 39008--39053 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
38998 ATGCTTTTAA
39008 AT AT AT AT AT AT AT 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 AT AT AT AT
39050 -T AT A
1 AT AT A
39054 CATTTCCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40771 original size:12 final size:13
Alignment explanation
Indices: 40754--40787 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40744 TGCATATGTA
40754 ATTTAAGT-ATTT
1 ATTTAAGTGATTT
40766 ATTTAAGTGATTT
1 ATTTAAGTGATTT
*
40779 AATTAAGTG
1 ATTTAAGTG
40788 CATCTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (13 bp):
ATTTAAGTGATTT
Found at i:51193 original size:17 final size:17
Alignment explanation
Indices: 51171--51306 Score: 139
Period size: 17 Copynumber: 7.9 Consensus size: 17
51161 AATTAAGATT
*
51171 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
51188 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
51205 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* * **
51223 TTGTAATCTTGAATGAAC
1 TAGT-TTAATGAATGAAC
51241 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
51258 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
*
51275 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
* *
51292 TA-CTTAATAAATGAA
1 TAGTTTAATGAATGAA
51307 GTGCATAGCT
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.11
17 63 0.62
18 27 0.27
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:51335 original size:87 final size:87
Alignment explanation
Indices: 51171--51326 Score: 203
Period size: 87 Copynumber: 1.8 Consensus size: 87
51161 AATTAAGATT
* * * * * * *
51171 TAGTTTAATAAATGAACTAGTTTAATTAATGAACTAACTTTATTCAATGAACTTGTAATCTTGAA
1 TAGTTTAATAAATGAACTAGTTTAATCAATGAACTAACTTTAATAAATGAACGTGCAAGCTTAAA
51236 TGAACTAGTTTAATGAATGAAC
66 TGAACTAGTTTAATGAATGAAC
*
51258 TAGTTTAATGAATGAACTAGTTTAATCAATGAACT-AC-TTAATAAATGAA-GTGCATAGC-TAA
1 TAGTTTAATAAATGAACTAGTTTAATCAATGAACTAACTTTAATAAATGAACGTGCA-AGCTTAA
51319 ATGAACTA
65 ATGAACTA
51327 AATGTTTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
84 13 0.22
85 12 0.20
86 2 0.03
87 33 0.55
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (87 bp):
TAGTTTAATAAATGAACTAGTTTAATCAATGAACTAACTTTAATAAATGAACGTGCAAGCTTAAA
TGAACTAGTTTAATGAATGAAC
Found at i:63184 original size:12 final size:12
Alignment explanation
Indices: 63163--63213 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
63153 ACCTTAAAAG
*
63163 ACAAGGAAAATA
1 ACAAGTAAAATA
63175 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
*
63188 TACAA-AAAAATGA
1 -ACAAGTAAAAT-A
63201 ACAAGTAAAATA
1 ACAAGTAAAATA
63213 A
1 A
63214 AAATGCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:71798 original size:11 final size:11
Alignment explanation
Indices: 71782--71807 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
71772 GTATGCACAT
71782 CATTTTAGTTG
1 CATTTTAGTTG
71793 CATTTTAGTTG
1 CATTTTAGTTG
71804 CATT
1 CATT
71808 AGATTGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.12, G:0.15, T:0.54
Consensus pattern (11 bp):
CATTTTAGTTG
Found at i:75028 original size:22 final size:21
Alignment explanation
Indices: 75003--75046 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
74993 GGTTGGATAT
*
75003 TCTAGATCATTTTG-AGGATGAA
1 TCTAGA-CAATTTGAAGG-TGAA
75025 TCTAGACAATTTGAAGGTGAA
1 TCTAGACAATTTGAAGGTGAA
75046 T
1 T
75047 TTGGCCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (21 bp):
TCTAGACAATTTGAAGGTGAA
Found at i:75590 original size:17 final size:17
Alignment explanation
Indices: 75568--75670 Score: 72
Period size: 17 Copynumber: 6.1 Consensus size: 17
75558 AATTAAGAGT
*
75568 TAGTTTAATAAATGAAC
1 TAGTTTAATCAATGAAC
* *
75585 TAGTTTGATGAATGAAC
1 TAGTTTAATCAATGAAC
*
75602 T--TTAAAT-AATGAAC
1 TAGTTTAATCAATGAAC
* *
75616 TAGCTTTATTCATTGAAC
1 TAG-TTTAATCAATGAAC
*
75634 T--TGTAATCTTGAATGAAC
1 TAGTTTAATC---AATGAAC
75652 TAGTTTAATCAATGAAC
1 TAGTTTAATCAATGAAC
75669 TA
1 TA
75671 CTTAGTTAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
14 8 0.12
15 9 0.14
17 29 0.44
18 14 0.21
20 6 0.09
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATCAATGAAC
Done.