Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009358.1 Hibiscus syriacus cultivar Beakdansim tig00113175_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: 67524
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1225 original size:13 final size:14
Alignment explanation
Indices: 1209--1243 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1199 ATTGTTTAAT
1209 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
1222 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1236 TGATTTGT
1 TGATTTGT
1244 GTATTGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1364 original size:19 final size:19
Alignment explanation
Indices: 1348--1449 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1338 AAAAATGACT
1348 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1367 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1386 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1400 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1419 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1439 ATCGCAATGCG
1 ATCGCAATGCG
1450 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1502 original size:19 final size:19
Alignment explanation
Indices: 1478--1769 Score: 374
Period size: 19 Copynumber: 16.4 Consensus size: 19
1468 GATTATCTCG
1478 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1497 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1516 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
1530 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1549 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1568 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1587 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1606 -TGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1624 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1643 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1657 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1676 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1695 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1709 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1729 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1743 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1762 TTGCGATT
1 TTGCGATT
1770 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 10, Indels: 44
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.12
16 23 0.10
17 19 0.08
18 21 0.09
19 137 0.57
20 12 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1518 original size:52 final size:52
Alignment explanation
Indices: 1456--1769 Score: 306
Period size: 52 Copynumber: 5.9 Consensus size: 52
1446 TGCGTTTATA
1456 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1508 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1560 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA-TGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1616 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * *
1668 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* * *
1720 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTCATTTCGCATTGCGATT
1770 GTATTTTCCG
Statistics
Matches: 228, Mismatches: 16, Indels: 35
0.82 0.06 0.13
Matches are distributed among these distances:
45 4 0.02
46 1 0.00
47 4 0.02
48 1 0.00
49 1 0.00
50 4 0.02
52 103 0.45
53 28 0.12
54 10 0.04
55 10 0.04
56 43 0.19
57 19 0.08
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1626 original size:127 final size:122
Alignment explanation
Indices: 1478--1741 Score: 185
Period size: 127 Copynumber: 2.1 Consensus size: 122
1468 GATTATCTCG
* *
1478 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TATCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TATCG--TTGCGATTTCATTTCGATTGCGATTTT
*
1540 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1604 CA
121 CA
* *
1606 -TGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGATTCT-A--TCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
1667 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
1727 CA
121 CA
1729 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1742 GTTGGGATTT
Statistics
Matches: 120, Mismatches: 6, Indels: 24
0.80 0.04 0.16
Matches are distributed among these distances:
120 7 0.06
121 4 0.03
122 18 0.15
123 5 0.04
124 15 0.12
125 4 0.03
127 67 0.56
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:4052 original size:12 final size:12
Alignment explanation
Indices: 4035--4059 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4025 TCTTCGGGGA
4035 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4047 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4059 C
1 C
4060 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4266 original size:23 final size:23
Alignment explanation
Indices: 4233--4277 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4223 TCTGAAACTC
4233 ATCAAAATCCGTG-TATTGACCAT
1 ATCAAAATCCG-GATATTGACCAT
*
4256 ATCAAAGTCCGGATATTGACCA
1 ATCAAAATCCGGATATTGACCA
4278 AGACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAAAATCCGGATATTGACCAT
Found at i:4984 original size:20 final size:20
Alignment explanation
Indices: 4956--5321 Score: 424
Period size: 20 Copynumber: 18.4 Consensus size: 20
4946 AAATTTAAGT
* * * *
4956 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
4976 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
4996 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5016 GTTGCGATTTAC-GATTA-TC
1 GTTGCGATTTACGGA-TACGC
5035 GTTGCGA-TTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5054 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5074 GTTGCGA-TTACGGATACGC
1 GTTGCGATTTACGGATACGC
5093 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5113 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5133 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5153 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
5173 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5193 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
5213 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
5233 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5253 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
5273 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
5293 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
5313 GTTGCGATT
1 GTTGCGATT
5322 ATGAAAATCG
Statistics
Matches: 304, Mismatches: 29, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
18 8 0.03
19 38 0.12
20 253 0.83
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:5332 original size:20 final size:20
Alignment explanation
Indices: 5289--5332 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5279 ATTTATGTGT
* * *
5289 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTATCAAAA
*
5309 TCGCGTTGCGATTATGAAAA
1 TCGCGTTGCGATTATCAAAA
5329 TCGC
1 TCGC
5333 AATGCGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTATCAAAA
Found at i:11225 original size:18 final size:18
Alignment explanation
Indices: 11202--11279 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 18
11192 CCGTGTAGAA
11202 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
11220 ATGTCCCGAAGGACCAAATATCACAT
1 ATGTCCCGAAGGA-C------CAC-T
*
11246 ATGTCCCGAAGGACCATT
1 ATGTCCCGAAGGACCACT
11264 ATGTCCCGAAGGACCA
1 ATGTCCCGAAGGACCA
11280 AATATCAGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
18 30 0.59
19 3 0.06
25 4 0.08
26 14 0.27
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:11252 original size:44 final size:44
Alignment explanation
Indices: 11202--11307 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
11192 CCGTGTAGAA
11202 ATGTCCCGAAGGACCACTATGTCCCGAAGGACCAAATATCACAT
1 ATGTCCCGAAGGACCACTATGTCCCGAAGGACCAAATATCACAT
* *
11246 ATGTCCCGAAGGACCATTATGTCCCGAAGGACCAAATATCAGAT
1 ATGTCCCGAAGGACCACTATGTCCCGAAGGACCAAATATCACAT
* * *
11290 ATTTCCTGAAAGACCACT
1 ATGTCCCGAAGGACCACT
11308 CCTTAAGAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (44 bp):
ATGTCCCGAAGGACCACTATGTCCCGAAGGACCAAATATCACAT
Found at i:11421 original size:23 final size:23
Alignment explanation
Indices: 11389--11432 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11379 ATTACATATA
*
11389 TGTCCTGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
11412 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
11433 CCCTCTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:14869 original size:20 final size:21
Alignment explanation
Indices: 14817--14872 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
14807 TACTGGAAGG
*
14817 GGGTATCGGTACCATAGTATA
1 GGGTATCGATACCATAGTATA
* * *
14838 GTAGTATTGATACCATGGTA-A
1 G-GGTATCGATACCATAGTATA
14859 GGGTATCGATACCA
1 GGGTATCGATACCA
14873 GGCCACATCG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 11 0.39
21 3 0.11
22 14 0.50
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCATAGTATA
Found at i:14910 original size:95 final size:95
Alignment explanation
Indices: 14745--14965 Score: 336
Period size: 95 Copynumber: 2.3 Consensus size: 95
14735 TGATTCAATC
*
14745 AGTATCGATACCATGGTAAGGGTATCGATATCAGGCAACATCGAACCTAAAATTGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGATAC
* * *
14810 TGGAAGGGGGTATCGGTACCATAGTATAGT
66 TGGAAGGGGATATCGATACCATAGTAGAGT
* * *
14840 AGTATTGATACCATGGTAAGGGTATCGATACCAGGCCACATCGAATCTAAAATTGGTATCGATAA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGAT-A
*
14905 C-GGAAGGGGATATCGATACCATAGTAGGGT
65 CTGGAAGGGGATATCGATACCATAGTAGAGT
* *
14935 AGTATCGATACCATGGTAGGGGTGTCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATAC
14966 TTAAGAGCCA
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
95 112 0.98
96 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGATAC
TGGAAGGGGATATCGATACCATAGTAGAGT
Found at i:14964 original size:20 final size:21
Alignment explanation
Indices: 14911--14965 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
14901 ATAACGGAAG
14911 GGGA-TATCGATACCATAGTA
1 GGGAGTATCGATACCATAGTA
*
14931 GGGTAGTATCGATACCATGGTA
1 GGG-AGTATCGATACCATAGTA
*
14953 GGG-GTGTCGATAC
1 GGGAGTATCGATAC
14966 TTAAGAGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
22 18 0.58
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGAGTATCGATACCATAGTA
Found at i:15513 original size:57 final size:58
Alignment explanation
Indices: 15296--15629 Score: 546
Period size: 57 Copynumber: 5.8 Consensus size: 58
15286 ATGGCACTAA
*
15296 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* **
15355 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTATATGAATTTTTGTATTGGGCACTTC
1 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
15414 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* *
15472 GTATGCAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTC
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* *
15529 GTGTGCAAAA-GTTAATAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* *
15586 GTGTGCAAATTGTTAAGACATTCATACTAAGTGTATGAATTTCC
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC
15630 ATATGGGAAA
Statistics
Matches: 260, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
57 108 0.42
58 89 0.34
59 63 0.24
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (58 bp):
GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
Found at i:15601 original size:115 final size:115
Alignment explanation
Indices: 15296--15629 Score: 535
Period size: 115 Copynumber: 2.9 Consensus size: 115
15286 ATGGCACTAA
*
15296 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGC
1 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* ** *
15361 AAAAATGTTAAGAAATTCATACTAAGTATATGAATTTTTGTATTGGGCACTTC
65 --AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTC
*
15414 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTATGCA
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCA
*
15479 AAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTC
66 AATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTC
* *
15529 GTGTGCAAAA-GTTAATAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCA
*
15593 AATTGTTAAGACATTCATACTAAGTGTATGAATTTCC
66 AA-TGTTAAGAAATTCATACTAAGTGTATGAATTTCC
15630 ATATGGGAAA
Statistics
Matches: 203, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
114 53 0.26
115 88 0.43
117 56 0.28
118 6 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (115 bp):
GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCA
AATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTC
Found at i:21236 original size:17 final size:18
Alignment explanation
Indices: 21208--21241 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21198 AATAATAACA
21208 TATATAATTTTTAAATTT
1 TATATAATTTTTAAATTT
21226 TATAT-ATTTTTAAATT
1 TATATAATTTTTAAATT
21242 GTTAGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATAATTTTTAAATTT
Found at i:22108 original size:17 final size:17
Alignment explanation
Indices: 22086--22127 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
22076 ATAAATTTAT
22086 AAAATATATTAAAAGTA
1 AAAATATATTAAAAGTA
**
22103 AAAATATATTATTAGTA
1 AAAATATATTAAAAGTA
22120 AAAATATA
1 AAAATATA
22128 AAAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAATATATTAAAAGTA
Found at i:26958 original size:31 final size:31
Alignment explanation
Indices: 26922--26981 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
26912 AACTTAAAAG
* *
26922 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
26953 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
26982 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:27059 original size:54 final size:54
Alignment explanation
Indices: 26995--27562 Score: 347
Period size: 54 Copynumber: 10.6 Consensus size: 54
26985 ACAACTACAA
26995 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
* * **
27049 TAATTAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCTATAC
** * ** * ** **
27106 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCTATAC
*
27161 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAAT-TCATA-
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATAC
* * ** * ** ** *
27214 T-TTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCTATAC
** * ** * ** ** *
27267 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATTTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCTATAC
* *
27322 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
* * * * * *
27370 AAATAAATTATTTAAAATAAATCAATCCATA--CT--AATAAAT-TATTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
*
27419 TAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATAC-ATAC
1 T-AATAAAT---TA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CTATAC
* *
27478 TAATAAATTATTTAAACTAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
*
27532 TAATAAATTATTTAAAATAAATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
27563 CAACTACAAT
Statistics
Matches: 409, Mismatches: 67, Indels: 76
0.74 0.12 0.14
Matches are distributed among these distances:
48 28 0.07
49 8 0.02
50 19 0.05
51 6 0.01
52 11 0.03
53 31 0.08
54 226 0.55
55 18 0.04
56 11 0.03
57 12 0.03
58 34 0.08
59 5 0.01
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
Found at i:27065 original size:32 final size:32
Alignment explanation
Indices: 27027--27191 Score: 166
Period size: 32 Copynumber: 5.7 Consensus size: 32
27017 CAATCCATAT
*
27027 TTTAAAATAAATCAATCTATACTAATTAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
* *
27059 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCTATACTAA-TAAATTA
27089 --T--AATAAATCAATC--TA-T-AT------
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
27107 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
27139 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
27171 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
27192 TTTTAAAATA
Statistics
Matches: 113, Mismatches: 4, Indels: 32
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.01
22 13 0.12
23 1 0.01
24 4 0.04
25 1 0.01
26 14 0.12
28 1 0.01
30 1 0.01
31 2 0.02
32 75 0.66
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:27136 original size:22 final size:23
Alignment explanation
Indices: 27061--27135 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
27051 ATTAATTATT
27061 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
27083 CTACAATAATAAATCAATCTATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
27109 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
27132 TAAA
1 TAAA
27136 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:27143 original size:80 final size:83
Alignment explanation
Indices: 26995--27638 Score: 778
Period size: 80 Copynumber: 7.9 Consensus size: 83
26985 ACAACTACAA
* *
26995 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATTAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
27060 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
* *
27081 -AACTACA-A-T-AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
*
27142 AAAATAAATCAATCTATAC
65 AAAATAAATCAATCCATAC
*
27161 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAAT---T-C------A-TAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
27215 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
27236 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
**
27301 TTAAAATAAATCAATTTATAC
63 TTAAAATAAATCAATCCATAC
* *
27322 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
27383 AAAATAAATCAATCCATAC
65 AAAATAAATCAATCCATAC
27402 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-C---C--AT--A-T-T
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
27457 TTAAAATAAATCAATACATAC
63 TTAAAATAAATCAATCCATAC
27478 TAATAAATTATTTAAACTAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TTAAA-TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
27543 TTAAAATAAATCAATTCATAC
63 TTAAAATAAATCAATCCATAC
*
27564 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
27625 AAAATAAATCAATC
65 AAAATAAATCAATC
27639 TATATTTTAA
Statistics
Matches: 500, Mismatches: 19, Indels: 84
0.83 0.03 0.14
Matches are distributed among these distances:
75 73 0.15
76 66 0.13
77 2 0.00
78 2 0.00
79 1 0.00
80 207 0.41
81 6 0.01
82 9 0.02
83 1 0.00
84 6 0.01
85 9 0.02
86 118 0.24
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (83 bp):
TAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
AAATAAATCAATCCATAC
Found at i:27146 original size:134 final size:127
Alignment explanation
Indices: 26995--27687 Score: 533
Period size: 134 Copynumber: 5.2 Consensus size: 127
26985 ACAACTACAA
*
26995 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATTAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-A-A-TCA-T-A-T-T
*
27060 TTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAATCTATATTTTAAAATAAATCAATC
59 TTAAAATAAATCAATCCATACAA-TAAAATAAATAAATCAATCTATATTTTAAAATAAATCAATC
27124 CATAC
123 CATAC
* ** *
27129 TAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATATT
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCAATC-ATATT
* ** * *
27194 TTAAAATAAATCAATTCATA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
59 TTAAAATAAATCAATCCATACAATAAAATAAATAAATCAAT-CT-AT--A-T-TTTAAAATAAAT
27258 CAATCCATA-
118 CAATCCATAC
** * ** * ** ** ** * **
27267 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATTTATACA-ACTACA
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCAAT-CATATTTTA
*** * * *
27329 ATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
62 A-AATAAATCAATCCATACAATAAAATAAATAAATCAAT-C---TATA-T-TTTAAAATAAATCA
27394 ATCCATAC
120 ATCCATAC
27402 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC---CATATTTTAAAAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATCATATTTTAAAAT
* *
27464 AAATCAATACATACTAATAAATTATTTAAACTAAATCAATCCATATTTTAAAATAAATCAATCCA
66 AAATCAATCCATAC-AATAAA--A--TAAA-TAAATCAATCTATATTTTAAAATAAATCAATCCA
27529 TAC
125 TAC
* *** * *
27532 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAAT-AATAAATCAATCCATATTTTAAA
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCAAT-CATATTTTAAA
*
27596 ATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATT
64 ATAAATCAATCCATAC-AATAAA--A--T-AAATAAATCAATCTATATTTTAAAATAAATCAATC
27661 CATAC
123 CATAC
27666 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
27688 TATTTTAAAA
Statistics
Matches: 458, Mismatches: 62, Indels: 78
0.77 0.10 0.13
Matches are distributed among these distances:
130 76 0.17
131 14 0.03
132 11 0.02
133 35 0.08
134 218 0.48
135 26 0.06
136 15 0.03
137 11 0.02
138 16 0.03
139 28 0.06
140 8 0.02
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (127 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATCATATTTTAAAAT
AAATCAATCCATACAATAAAATAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
Found at i:27149 original size:14 final size:14
Alignment explanation
Indices: 27130--27182 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
27120 AATCCATACT
27130 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
27144 AATAAATCAATCTATACT
1 AATAAAT-TAT-T-TA-A
27162 AATAAATTATTTAA
1 AATAAATTATTTAA
27176 AATAAAT
1 AATAAAT
27183 CAATCTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 2 0.06
17 4 0.13
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:27197 original size:22 final size:22
Alignment explanation
Indices: 27169--27234 Score: 102
Period size: 21 Copynumber: 3.1 Consensus size: 22
27159 ACTAATAAAT
27169 TATTTAAAATAAATCAATCT-A
1 TATTTAAAATAAATCAATCTCA
27190 TATTTTAAAATAAATCAAT-TCA
1 TA-TTTAAAATAAATCAATCTCA
27212 TATTTAAAATAAATCAATC-CA
1 TATTTAAAATAAATCAATCTCA
27233 TA
1 TA
27235 CTAATAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 23 0.55
22 19 0.45
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TATTTAAAATAAATCAATCTCA
Found at i:27272 original size:22 final size:22
Alignment explanation
Indices: 27246--27288 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
27236 TAATAAATTA
27246 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
27268 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
27289 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:27297 original size:22 final size:22
Alignment explanation
Indices: 27248--27296 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
27238 ATAAATTATT
**
27248 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
27270 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
27293 TAAA
1 TAAA
27297 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:27373 original size:18 final size:18
Alignment explanation
Indices: 27352--27409 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
27342 CCATATTTTA
27352 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
* *
27370 AAATAAAT-TAT--TTA-
1 AAATAAATCAATCCATAC
27384 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
*
27402 TAATAAAT
1 AAATAAAT
27410 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
17 4 0.13
18 15 0.48
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATCAATCCATAC
Found at i:27418 original size:241 final size:242
Alignment explanation
Indices: 26995--27638 Score: 1182
Period size: 241 Copynumber: 2.7 Consensus size: 242
26985 ACAACTACAA
* *
26995 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATTAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
27060 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
* *
27125 ATACTAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTA
131 ATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
* *
27190 TATTTTAAAATAAATCAATTCATA-TTTAAAATAAATCAATCCATAC
196 TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
27236 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
27301 TTAAAATAAATCAATTTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
27366 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
131 ATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
27431 TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
196 TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
*
27478 TAATAAATTATTTAAACTAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
27543 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
27608 ATACTAATAAATTATTTAAAATAAATCAATC
131 ATACTAATAAATTATTTAAAATAAATCAATC
27639 TATATTTTAA
Statistics
Matches: 389, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
241 210 0.54
242 179 0.46
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (242 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
Found at i:27485 original size:22 final size:22
Alignment explanation
Indices: 27412--27476 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
27402 TAATAAATTA
27412 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
27434 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
27456 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATCCATA
27477 CTAATAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:27514 original size:22 final size:22
Alignment explanation
Indices: 27488--27530 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
27478 TAATAAATTA
*
27488 TTTAAACTAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
27510 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
27531 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:27539 original size:22 final size:21
Alignment explanation
Indices: 27490--27539 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
27480 ATAAATTATT
**
27490 TAAACTAAATCAATCCATATTT
1 TAAA-TAAATCAATCCATATAA
27512 TAAAATAAATCAATCCATACTAA
1 T-AAATAAATCAATCCATA-TAA
27535 TAAAT
1 TAAAT
27540 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAATAAATCAATCCATATAA
Found at i:27619 original size:22 final size:22
Alignment explanation
Indices: 27544--27618 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
27534 ATAAATTATT
* *
27544 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
27566 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
27592 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
27615 TAAA
1 TAAA
27619 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:27644 original size:54 final size:54
Alignment explanation
Indices: 27090--27687 Score: 441
Period size: 54 Copynumber: 11.1 Consensus size: 54
27080 CAACTACAAT
*
27090 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** * *
27144 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAA
*
27198 AATAAATCAATTCATA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
27251 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** * ** ** * ** *
27305 AATAAATCAATTTATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
** **
27361 AATCCATACAAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** * ** *
27417 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** * ** * ** *
27469 AATACATACTAATAAAT-TATTTAAACTAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** ** * *
27523 AATCCATACTAATAAAT-TATTTAAAATAAATCAATTCATAC-AACTACA--A--T--
1 AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
27573 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
27627 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
27681 AATAAAT
1 AATAAAT
27688 TATTTTAAAA
Statistics
Matches: 445, Mismatches: 63, Indels: 72
0.77 0.11 0.12
Matches are distributed among these distances:
47 10 0.02
48 32 0.07
49 6 0.01
50 7 0.02
51 2 0.00
52 12 0.03
53 31 0.07
54 262 0.59
55 22 0.05
56 11 0.02
57 14 0.03
58 23 0.05
59 3 0.01
60 10 0.02
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:27696 original size:15 final size:15
Alignment explanation
Indices: 27667--27784 Score: 121
Period size: 15 Copynumber: 7.5 Consensus size: 15
27657 AATTCATACT
27667 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
27681 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
27696 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
27718 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
27733 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
*
27748 AATAAATTATTGTAA
1 AATAAATTATTTTAA
27763 AATAAATTATTTTAA
1 AATAAATTATTTTAA
27778 AATAAAT
1 AATAAAT
27785 AACCTTATTA
Statistics
Matches: 86, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.10
15 60 0.70
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.12
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:27713 original size:69 final size:67
Alignment explanation
Indices: 27613--27769 Score: 194
Period size: 69 Copynumber: 2.3 Consensus size: 67
27603 AATCCATACT
*
27613 AATAAATTA-TTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAA-TAAATTA
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAATT-ATA--AAGTAAATTA
27676 -TTTAA
62 TTTTAA
* ** *
27681 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAGTAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAGTAAATTATTTT
*
27746 AT
66 AA
*
27748 AATAAATTATTGTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
27770 TATTTTAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
65 2 0.03
66 7 0.09
67 27 0.34
68 15 0.19
69 28 0.35
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAGTAAATTATTTT
AA
Found at i:27726 original size:47 final size:49
Alignment explanation
Indices: 27373--27754 Score: 187
Period size: 54 Copynumber: 7.4 Consensus size: 49
27363 TCCATACAAA
*
27373 TAAATTA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTT---ATAAAG
* * **
27423 TCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAA-
1 TAAAT---TATTTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTATA--AAG
* * **
27481 TAAATTA-TTTAAACTAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-
1 TAAATTATTTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTATA--AAG
* ** *
27535 TAAATTA-TTTAAAATAAATCAATTCATAC-AACTACAATAATAAATCAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTATAAAG
** *
27583 TCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTT---ATAAAG
* * *
27633 TCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTA-AAA-
1 T-AA-AT-TATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
**
27683 TAAATTATTTTAAAATAAATCAATCCATA-TTTTATAATAATTTATTTTAAAG
1 TAAATTATTTTAAAATAAATCAATCCATACTAATA-AATAATTTA---TAAAG
*
27735 TAAATTATTTTATAATAAAT
1 TAAATTATTTTAAAATAAAT
27755 TATTGTAAAA
Statistics
Matches: 273, Mismatches: 31, Indels: 54
0.76 0.09 0.15
Matches are distributed among these distances:
46 3 0.01
47 38 0.14
48 28 0.10
49 6 0.02
50 20 0.07
51 7 0.03
52 19 0.07
53 2 0.01
54 129 0.47
55 2 0.01
56 4 0.01
58 13 0.05
59 2 0.01
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (49 bp):
TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
Found at i:27823 original size:18 final size:17
Alignment explanation
Indices: 27667--27832 Score: 77
Period size: 15 Copynumber: 9.8 Consensus size: 17
27657 AATTCATACT
27667 AATAAATTA-TTT-A-A
1 AATAAATTATTTTAATA
27681 AATAAATTATTTTAAAATA
1 AATAAATTATTTT--AATA
*
27700 AATCAATCCATATTTT-AT-
1 AATAAAT---TATTTTAATA
*
27718 AATAATTTATTTT-A-A
1 AATAAATTATTTTAATA
*
27733 AGTAAATTATTTT-AT-
1 AATAAATTATTTTAATA
*
27748 AATAAATTATTGT-A-A
1 AATAAATTATTTTAATA
27763 AATAAATTATTTTAAAATA
1 AATAAATTATTTT--AATA
* *
27782 AATAACCTTA-TTAAATTA
1 AATAA-ATTATTTTAA-TA
**
27800 TTTAAAATTATTTTAATA
1 AAT-AAATTATTTTAATA
27818 AATAAATATATTTTA
1 AATAAAT-TATTTTA
27833 TAATTGTTCT
Statistics
Matches: 116, Mismatches: 16, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
14 9 0.08
15 46 0.40
17 6 0.05
18 23 0.20
19 23 0.20
20 3 0.03
22 6 0.05
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (17 bp):
AATAAATTATTTTAATA
Found at i:29476 original size:20 final size:19
Alignment explanation
Indices: 29436--29476 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29426 CAGTAAAAAA
*
29436 TTACTAAAAATATTATTTT
1 TTACTAAAAATATTATATT
*
29455 TTACTTAAAATATTAATATT
1 TTACTAAAAATATT-ATATT
29475 TT
1 TT
29477 TTAACATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTACTAAAAATATTATATT
Found at i:29606 original size:21 final size:21
Alignment explanation
Indices: 29580--29620 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
29570 GTAAAGCCTC
29580 AATAATAATATTTTAGGTAAA
1 AATAATAATATTTTAGGTAAA
29601 AATAATAATATTTTAGGTAA
1 AATAATAATATTTTAGGTAA
29621 TTTTTTACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (21 bp):
AATAATAATATTTTAGGTAAA
Found at i:30678 original size:31 final size:31
Alignment explanation
Indices: 30638--30723 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
30628 AAATTATGTA
*
30638 TTTAGTACCTAAACTATTAGTTTTAGTCTAT
1 TTTAGTACCTAAACTATTAGTTTTAGTCTAC
*
30669 TTTAATACCTAAACTATTAGTTTTAGTCTAC
1 TTTAGTACCTAAACTATTAGTTTTAGTCTAC
*
30700 TTTAGTACTTAAACT-TTCAGTTTT
1 TTTAGTACCTAAACTATT-AGTTTT
30724 CTTAAACCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 2 0.04
31 48 0.96
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTAGTACCTAAACTATTAGTTTTAGTCTAC
Found at i:33042 original size:20 final size:20
Alignment explanation
Indices: 33017--33067 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
33007 CCTATAGGGA
33017 GTATCGATACTCAACCCTTG
1 GTATCGATACTCAACCCTTG
*
33037 GTATCGATACTCGACCCTTG
1 GTATCGATACTCAACCCTTG
33057 GTATCGATACT
1 GTATCGATACT
33068 TCCATGAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCAACCCTTG
Found at i:41453 original size:30 final size:30
Alignment explanation
Indices: 41413--41469 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
41403 GGAGAGGTTC
* * *
41413 TAGAAATTTCTATAGCTTTCTGGAGAAGTG
1 TAGAAATTTCTAGAACATTCTGGAGAAGTG
*
41443 TAGAATTTTCTAGAACATTCTGGAGAA
1 TAGAAATTTCTAGAACATTCTGGAGAA
41470 CTCTAGAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (30 bp):
TAGAAATTTCTAGAACATTCTGGAGAAGTG
Found at i:45858 original size:8 final size:8
Alignment explanation
Indices: 45842--45874 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
45832 TAGCACTACC
*
45842 TTCCGTTT
1 TTCCCTTT
45850 TTCCCTTT
1 TTCCCTTT
45858 TTCCCTTT
1 TTCCCTTT
45866 TTCCCTTT
1 TTCCCTTT
45874 T
1 T
45875 ATCCACTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (8 bp):
TTCCCTTT
Found at i:47481 original size:21 final size:21
Alignment explanation
Indices: 47452--47510 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
47442 ACTGAGTTGG
47452 TATCGATATTGAACCTATTAC
1 TATCGATATTGAACCTATTAC
* *
47473 TATCAATATTGACCCTATTAC
1 TATCGATATTGAACCTATTAC
*
47494 TATCGATACTG-ACCTAT
1 TATCGATATTGAACCTAT
47511 GAGTATCAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (21 bp):
TATCGATATTGAACCTATTAC
Found at i:49740 original size:31 final size:32
Alignment explanation
Indices: 49700--49817 Score: 114
Period size: 31 Copynumber: 3.8 Consensus size: 32
49690 AAGGGAGTAC
* *
49700 CTTGAGGCCTTAGAGCCTACCCAA-GAAATAT
1 CTTGGGGCCTAAGAGCCTACCCAATGAAATAT
* * * ** *
49731 CTTGGGGCCTCAGATCCTA-CTAATGAAGCAC
1 CTTGGGGCCTAAGAGCCTACCCAATGAAATAT
* * *
49762 CTTGGGGCCTGAGAACCTACCCAATGGAATAT
1 CTTGGGGCCTAAGAGCCTACCCAATGAAATAT
*
49794 CTCGGGGCCTAAGAGCCTACCCAA
1 CTTGGGGCCTAAGAGCCTACCCAA
49818 GGGTCACCTT
Statistics
Matches: 68, Mismatches: 17, Indels: 3
0.77 0.19 0.03
Matches are distributed among these distances:
30 3 0.04
31 37 0.54
32 28 0.41
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (32 bp):
CTTGGGGCCTAAGAGCCTACCCAATGAAATAT
Found at i:52772 original size:11 final size:11
Alignment explanation
Indices: 52756--52805 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
52746 GATAAAGAAA
52756 TAATTTTTTAT
1 TAATTTTTTAT
*
52767 TAATTTTTTTT
1 TAATTTTTTAT
* *
52778 TAATTATTAATT
1 TAATTTTTTA-T
52790 TAATATTTTTAT
1 TAAT-TTTTTAT
52802 TAAT
1 TAAT
52806 CATTTTTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 17 0.55
12 10 0.32
13 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTTAT
Found at i:59192 original size:19 final size:19
Alignment explanation
Indices: 59159--59205 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
59149 CAATTGGTGC
59159 ATCGATGCA-AAGGAGTGT
1 ATCGATGCATAAGGAGTGT
59177 ATCGATGCATAAGGAGTGT
1 ATCGATGCATAAGGAGTGT
59196 ATCGATGCAT
1 ATCGATGCAT
59206 CACAACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (19 bp):
ATCGATGCATAAGGAGTGT
Found at i:59756 original size:15 final size:15
Alignment explanation
Indices: 59738--59770 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
59728 GAGGGTATAA
59738 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
59753 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
59768 TAG
1 TAG
59771 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Done.