Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008474.1 Hibiscus syriacus cultivar Beakdansim tig00111302_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: 115817
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4363 original size:29 final size:29
Alignment explanation
Indices: 4321--4379 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4311 ATTTTCACCT
4321 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
4350 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
4379 A
1 A
4380 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:8056 original size:21 final size:23
Alignment explanation
Indices: 8032--8075 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8022 TTTTTTGTAA
8032 TTTA-AAAGA-AATAAGATTTTT
1 TTTATAAAGATAATAAGATTTTT
* *
8053 TTTATAAATATAATAATATTTTT
1 TTTATAAAGATAATAAGATTTTT
8076 AAAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TTTATAAAGATAATAAGATTTTT
Found at i:8093 original size:14 final size:13
Alignment explanation
Indices: 8069--8107 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
8059 AATATAATAA
8069 TATTTTTAAAATT
1 TATTTTTAAAATT
*
8082 TATTTTTAAAAAT
1 TATTTTTAAAATT
* *
8095 AAATTTTAAAATT
1 TATTTTTAAAATT
8108 ACCAGATTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTTTTAAAATT
Found at i:9769 original size:21 final size:21
Alignment explanation
Indices: 9743--9792 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
9733 CACTCTTATT
*
9743 CTCTTCCTTCGGCGGTTCTGA
1 CTCTTCCTTAGGCGGTTCTGA
9764 CTCTTCCTTAGGCGGTTCTGA
1 CTCTTCCTTAGGCGGTTCTGA
9785 CTCTTCCT
1 CTCTTCCT
9793 CGTTGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.34, G:0.20, T:0.40
Consensus pattern (21 bp):
CTCTTCCTTAGGCGGTTCTGA
Found at i:28152 original size:20 final size:19
Alignment explanation
Indices: 28127--28180 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
28117 GCGAAATAAA
28127 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
28147 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
28167 AATCGCAACGCGAT
1 AATCGCAACGCGAT
28181 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:28242 original size:21 final size:21
Alignment explanation
Indices: 28127--28242 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 21
28117 GCGAAATAAA
*
28127 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
28147 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* **
28167 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* * ** *
28188 AATCACAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
28208 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
28230 AATCGCAACGCGA
1 AATCGCAACGCGA
28243 ACATATAAAT
Statistics
Matches: 68, Mismatches: 24, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 25 0.37
21 40 0.59
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:28315 original size:20 final size:20
Alignment explanation
Indices: 28271--28566 Score: 251
Period size: 20 Copynumber: 14.6 Consensus size: 20
28261 GATTCTGACT
*
28271 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
28292 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
28312 ATCGCAACGAC-AATACATAAA
1 ATCGCAACG-CGTATCCGT-AA
*
28333 ATCGCAACGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
* *
28353 ATCGCAACGCG-ATTC-TGACT
1 ATCGCAACGCGTATCCGT-A-A
*
28373 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
28394 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* ***
28414 ATCGCAACGAC-AATACAAAAA
1 ATCGCAACG-CGTAT-CCGTAA
*
28435 ATCGCAACGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
* * *
28455 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
28475 ATCGCAACGCATATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
28495 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
28515 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
28535 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
28556 ATCGCAACGCG
1 ATCGCAACGCG
28567 ATTTTTAAAG
Statistics
Matches: 221, Mismatches: 41, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 133 0.60
21 81 0.37
22 2 0.01
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:28316 original size:41 final size:40
Alignment explanation
Indices: 28271--28566 Score: 283
Period size: 41 Copynumber: 7.3 Consensus size: 40
28261 GATTCTGACT
* * *
28271 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGAGAATCCGTAA
* * * * * *
28312 ATCGCAACGAC-AATACATAAAATCGCAACGCGTATCCATAA
1 ATCGCAACG-CGTATCCGT-AAATCGCAACGAGAATCCGTAA
* * *
28353 ATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATCCGT-AA
* ***
28394 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACAAAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAAT-CCGTAA
* *
28435 ATCGCAACGCGTATCCATAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATCCGTAA
* * *
28475 ATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATCCGTAA
* * *
28515 ATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATCCGT-AA
28556 ATCGCAACGCG
1 ATCGCAACGCG
28567 ATTTTTAAAG
Statistics
Matches: 216, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.01
40 93 0.43
41 115 0.53
42 5 0.02
43 1 0.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATCCGTAA
Found at i:28354 original size:102 final size:102
Alignment explanation
Indices: 28230--28463 Score: 425
Period size: 102 Copynumber: 2.3 Consensus size: 102
28220 GATTTTCCAG
* *
28230 AATCGCAACGCG-AACATATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAAT
1 AATCGCAACGCGTATC-CATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAAT
*
28294 CGCAACGCGTATCCGTAAATCGCAACGACAATACATAA
65 CGCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
28332 AATCGCAACGCGTATCCATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAATC
1 AATCGCAACGCGTATCCATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAATC
28397 GCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
66 GCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
28434 AATCGCAACGCGTATCCATAAATCGCAACG
1 AATCGCAACGCGTATCCATAAATCGCAACG
28464 AGAATACGTA
Statistics
Matches: 128, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 126 0.98
103 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (102 bp):
AATCGCAACGCGTATCCATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAATC
GCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
Found at i:28479 original size:102 final size:102
Alignment explanation
Indices: 28230--28521 Score: 396
Period size: 102 Copynumber: 2.9 Consensus size: 102
28220 GATTTTCCAG
* * * * *
28230 AATCGCAACGCG-AACATATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAAT
1 AATCGCAACGCGTATC-CATAAATCGCAACGAGATACTGACAATCGCAACGAGTATCCGTAAAAT
*
28294 CGCAACGCGTATCCGTAAATCGCAACGACAATACATAA
65 CGCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
* * *
28332 AATCGCAACGCGTATCCATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAATC
1 AATCGCAACGCGTATCCATAAATCGCAACGAGATACTGACAATCGCAACGAGTATCCGTAAAATC
28397 GCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
66 GCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
*
28434 AATCGCAACGCGTATCCATAAATCGCAACGAGAATAC-GTA-AATCGCAACGCA-TATCTGT-AA
1 AATCGCAACGCGTATCCATAAATCGCAACGAG-ATACTG-ACAATCGCAACG-AGTATCCGTAAA
* * *
28495 ATCGCAACGAGAATACGTAAATCGCAA
63 ATCGCAACGCGTATCCGTAAATCGCAA
28522 TGCGTATCCG
Statistics
Matches: 176, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
101 26 0.15
102 143 0.81
103 7 0.04
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (102 bp):
AATCGCAACGCGTATCCATAAATCGCAACGAGATACTGACAATCGCAACGAGTATCCGTAAAATC
GCAACGCGTATCCGTAAATCGCAACGACAATACAAAA
Found at i:28588 original size:80 final size:80
Alignment explanation
Indices: 28373--28565 Score: 242
Period size: 81 Copynumber: 2.4 Consensus size: 80
28363 GATTCTGACT
** * * * * * **
28373 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACAAAAAATC
1 ATCGCAACGACAATACGT-AAATCGCAACGCATATCTGTAAAGCGCAACGAGAATAC-GTAAATC
28438 GCAACGCGTATCCATAA
64 GCAACGCGTATCCATAA
* *
28455 ATCGCAACGAGAATACGTAAATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAAATCGC
1 ATCGCAACGACAATACGTAAATCGCAACGCATATCTGTAAAGCGCAACGAGAATACGTAAATCGC
* *
28520 AATGCGTATCCGTAA
66 AACGCGTATCCATAA
28535 ATCGCAACGACAATACGTAAAATCGCAACGC
1 ATCGCAACGACAATACGT-AAATCGCAACGC
28566 GATTTTTAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 37 0.37
81 47 0.47
82 16 0.16
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (80 bp):
ATCGCAACGACAATACGTAAATCGCAACGCATATCTGTAAAGCGCAACGAGAATACGTAAATCGC
AACGCGTATCCATAA
Found at i:29163 original size:21 final size:21
Alignment explanation
Indices: 29102--29180 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
29092 TTCTAAACTT
29102 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
29122 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
29142 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
29163 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
29181 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:29241 original size:14 final size:14
Alignment explanation
Indices: 29222--29277 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
29212 TTTAATTTCG
29222 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
29236 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
29255 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
29269 CGTTGCGAT
1 CGTTGCGAT
29278 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29247 original size:33 final size:33
Alignment explanation
Indices: 29205--29277 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
29195 CAAAATCGCA
29205 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
*
29238 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
29271 TTGCGAT
1 TTGCGAT
29278 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
Found at i:29284 original size:33 final size:33
Alignment explanation
Indices: 29216--29297 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
29206 TGCGATTTTA
**
29216 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
29249 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
*
29282 ATTTCCGCATTGCGAT
1 ATTT-CGCGTTGCGAT
29298 AGTCATTCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 35 0.78
34 10 0.22
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
Found at i:29324 original size:20 final size:20
Alignment explanation
Indices: 29262--29317 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
29252 TCGCGTTGCG
29262 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
29282 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATAGTC
29302 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
29318 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.75
21 2 0.06
22 2 0.06
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:31183 original size:94 final size:94
Alignment explanation
Indices: 31022--31401 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
31012 TAGATTGCTT
* * * *
31022 AGTAAATTTATTCGGTTACTACCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
31087 ATTTTTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
31116 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAGTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
31181 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
31210 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACAGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
31275 ATTTGTCTTTGTTTTTTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
31304 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
31369 ATTTGTCTTTGTTTTGTCTTTTGGTT-AA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31397 AGTAA
1 AGTAA
31402 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 27 0.10
94 244 0.90
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31540 original size:14 final size:14
Alignment explanation
Indices: 31523--31549 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31513 AACGCGAAAC
31523 CAAAATCGCAACGA
1 CAAAATCGCAACGA
31537 CAAAATCGCAACG
1 CAAAATCGCAACG
31550 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:31547 original size:33 final size:33
Alignment explanation
Indices: 31505--31568 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
31495 ACGAGAAATG
31505 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
31538 AAAATCGCAACGCGAAACCAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAATCGCAACG
31569 CGAAACTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.30, G:0.16, T:0.06
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:31583 original size:19 final size:19
Alignment explanation
Indices: 31489--31574 Score: 110
Period size: 19 Copynumber: 4.8 Consensus size: 19
31479 AAAAATGACT
* **
31489 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAACCAAA
31508 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
31527 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAACCAAA
31541 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
31560 ATCGCAACGCGAAAC
1 ATCGCAACGCGAAAC
31575 TATAATCGCG
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.19
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 42 0.71
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (19 bp):
ATCGCAACGCGAAACCAAA
Found at i:31643 original size:20 final size:20
Alignment explanation
Indices: 31618--31704 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
31608 GATTCTCTCG
*
31618 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
31638 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
31658 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
31678 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
31698 TTGCGAT
1 TTGCGAT
31705 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.06
20 58 0.94
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:33668 original size:14 final size:14
Alignment explanation
Indices: 33649--33684 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
33639 ATTGTTTAAT
33649 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
33663 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
33677 TGATTTGT
1 TGATTTGT
33685 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:33925 original size:33 final size:33
Alignment explanation
Indices: 33869--33958 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
33859 TTCGCATTGT
*
33869 GATTTTCATTTTCGCATTTCGATTCACTCGTTGC
1 GATTTTCA-TTTCGCATTGCGATTCACTCGTTGC
*
33903 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCACTCGTTGC
** *
33936 GATAGTCATTTCCGCGTTGCGAT
1 GATTTTCATTT-CGCATTGCGAT
33959 AGTCAATTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 32 0.64
34 18 0.36
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCACTCGTTGC
Found at i:33955 original size:20 final size:19
Alignment explanation
Indices: 33930--34018 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 19
33920 GCGATTCTCT
33930 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
33950 CGTTGCGATAGTCAATTTCG
1 CGTTGCGATAGTC-ATTTCG
*
33970 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
33990 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
*
34010 TGTTGCGAT
1 CGTTGCGAT
34019 TTCCGTGTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.06
20 53 0.84
21 6 0.10
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:34016 original size:40 final size:40
Alignment explanation
Indices: 33930--34018 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
33920 GCGATTCTCT
33930 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATTTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATTTCG
* *
33970 CATTGCGATAGTCATTTCCGTGTTGCGATAGTC-ATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAAT-TTCG
*
34010 TGTTGCGAT
1 CGTTGCGAT
34019 TTCCGTGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.05
40 42 0.95
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATTTCG
Found at i:36485 original size:24 final size:24
Alignment explanation
Indices: 36451--36504 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36441 CTGAAAAATC
36451 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
36475 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
36499 ATCAAA
1 ATCAAA
36505 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:37388 original size:20 final size:20
Alignment explanation
Indices: 37365--37550 Score: 196
Period size: 20 Copynumber: 9.2 Consensus size: 20
37355 GGAGATCGCA
37365 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
37385 TTGCGATTTTACGTAT-TGTCA
1 TTGCGA-TTTACGGATACG-CG
*
37406 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
* * *
37426 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
*
37446 TTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCG
37466 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
37486 TTACGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
37507 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
*
37527 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACGCG
37548 TTG
1 TTG
37551 AGATAGTCAG
Statistics
Matches: 136, Mismatches: 23, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
20 89 0.65
21 47 0.35
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:37389 original size:40 final size:39
Alignment explanation
Indices: 37345--37577 Score: 145
Period size: 41 Copynumber: 5.7 Consensus size: 39
37335 GGAAACTGAT
37345 TTGCGA-TACCGGAGATCGCATTGCGATTTACGGATACGCG
1 TTGCGATTA-CGGA-ATCGCATTGCGATTTACGGATACGCG
* * *
37385 TTGCGATTTTAC-GTATTGTCATTGCGATTTACGGATACGCA
1 TTGCGA--TTACGGAATCG-CATTGCGATTTACGGATACGCG
* * * * *
37426 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGA-TTACGGAATCGCATTGCGATTTACGGATACGCG
* * * *
37466 TTGCGATTTACGG-ATACGCGTTACGATTTTACGTAT-TGTCG
1 TTGCGA-TTACGGAAT-CGCATTGCGA-TTTACGGATACG-CG
*
37507 TTGCGATTTACGG-ATACGCATTGCGATTTTACGGATACTCG
1 TTGCGA-TTACGGAAT-CGCATTGCGA-TTTACGGATACGCG
* * *
37548 TTGAGA-TAGTCAGAATCGCGTTGCGATTTA
1 TTGCGATTA--CGGAATCGCATTGCGATTTA
37578 TATGTTCGCG
Statistics
Matches: 155, Mismatches: 26, Indels: 24
0.76 0.13 0.12
Matches are distributed among these distances:
39 3 0.02
40 58 0.37
41 89 0.57
42 3 0.02
43 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (39 bp):
TTGCGATTACGGAATCGCATTGCGATTTACGGATACGCG
Found at i:37410 original size:41 final size:41
Alignment explanation
Indices: 37363--37550 Score: 186
Period size: 41 Copynumber: 4.6 Consensus size: 41
37353 CCGGAGATCG
*
37363 CATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
37404 CATTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * * *
37444 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGGATACG
1 CATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * * * * *
37484 CGTTACGATTTTACGTAT-TGTCGTTGCGA-TTTACGGATACG
1 CATTGCGA-TTTACGGATACG-CGTTGCGATTTTACGTATTCT
*
37525 CATTGCGATTTTACGGATACTCGTTG
1 CATTGCGA-TTTACGGATACGCGTTG
37551 AGATAGTCAG
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
40 53 0.42
41 74 0.58
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:37570 original size:61 final size:61
Alignment explanation
Indices: 37404--37577 Score: 178
Period size: 61 Copynumber: 2.9 Consensus size: 61
37394 TACGTATTGT
* * * *
37404 CATTGCGATTTACGGATACGCATTGCGAT-TTACGTATTC-TCGTTGCGATTTACAGATACG
1 CATTGCGATTTACGGATACGCGTTACGATGTCACG-AATCGTCGTTGCGATTTACAGATACG
* * * * * *
37464 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CATTGCGATTTACGGATACGCGTTACGATGTCACGAATCGTCGTTGCGATTTACAGATACG
*
37525 CATTGCGATTTTACGGATACTCGTTGA-GATAGTCA-GAATCG-CGTTGCGATTTA
1 CATTGCGA-TTTACGGATACGCGTT-ACGAT-GTCACGAATCGTCGTTGCGATTTA
37578 TATGTTCGCG
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
60 27 0.28
61 44 0.46
62 22 0.23
63 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (61 bp):
CATTGCGATTTACGGATACGCGTTACGATGTCACGAATCGTCGTTGCGATTTACAGATACG
Found at i:37586 original size:20 final size:20
Alignment explanation
Indices: 37563--37615 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
37553 ATAGTCAGAA
*
37563 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
37583 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
37603 TCGCGTTGCGATT
1 TCGCGTTGCGATT
37616 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:37676 original size:42 final size:42
Alignment explanation
Indices: 37583--37676 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
37573 ATTTATATGT
* *
37583 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
37624 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
37666 TCGCGTTGCGA
1 TCGCGTTGCGA
37677 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:37714 original size:20 final size:19
Alignment explanation
Indices: 37665--37715 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
37655 ATTCTTCATA
37665 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
37684 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
37705 ATCGCGTTGCG
1 ATCGCGTTGCG
37716 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:42117 original size:79 final size:79
Alignment explanation
Indices: 41986--42143 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 79
41976 TTTCACAAGC
* * * *
41986 GATTAAGTAATCAATGACAACTAAGAAGGTTGTTAATTATTCATATTAATACATGACATATTTTG
1 GATTAAGTAAACAAGGACAACTAAGAAGGGTGTTAATTATTCATATTAATACATGACATATTTTA
42051 AACTAAAA-TTGATT
66 AAC-AAAATTTGATT
42065 GATTAAGTAAACAAGGACAACTAAGAAGGGTGTTAATTATTCATATTAATACATGACATATTTTA
1 GATTAAGTAAACAAGGACAACTAAGAAGGGTGTTAATTATTCATATTAATACATGACATATTTTA
42130 AACAAAATTTGATT
66 AACAAAATTTGATT
42144 TATTTTTGTT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
78 4 0.05
79 70 0.95
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (79 bp):
GATTAAGTAAACAAGGACAACTAAGAAGGGTGTTAATTATTCATATTAATACATGACATATTTTA
AACAAAATTTGATT
Found at i:47414 original size:21 final size:21
Alignment explanation
Indices: 47388--47427 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47378 TTGTCATAAC
* *
47388 CATTTTTTAAAAGCAATTAAA
1 CATTTTTAAAAAACAATTAAA
47409 CATTTTTAAAAAACAATTA
1 CATTTTTAAAAAACAATTA
47428 TGATTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
CATTTTTAAAAAACAATTAAA
Found at i:48142 original size:22 final size:20
Alignment explanation
Indices: 48114--48280 Score: 86
Period size: 20 Copynumber: 8.2 Consensus size: 20
48104 AGAAGTCGAA
*
48114 TTCGCAACTTGAATTTGACATT
1 TTCGCAACTCGAATTT--CATT
* *
48136 TTCGCAACACGAATTTCTTT
1 TTCGCAACTCGAATTTCATT
* * **
48156 TTCGCAACTCGATTTTTAAA
1 TTCGCAACTCGAATTTCATT
* * *
48176 TTCGCAACACGAGTTTCGTT
1 TTCGCAACTCGAATTTCATT
** ** **
48196 TTCTTAACTCGAAAAATCAAA
1 TTCGCAACTCG-AATTTCATT
48217 TTCGCAACTCGAATTTTCATT
1 TTCGCAACTCGAA-TTTCATT
** * *
48238 TTCG-AGTTGGATTTTCATT
1 TTCGCAACTCGAATTTCATT
*
48257 TTCG-AATTGCGAATTTCATT
1 TTCGCAACT-CGAATTTCATT
48277 TTCG
1 TTCG
48281 AGTTGTGATT
Statistics
Matches: 105, Mismatches: 37, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
19 14 0.13
20 58 0.55
21 19 0.18
22 14 0.13
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (20 bp):
TTCGCAACTCGAATTTCATT
Found at i:48160 original size:42 final size:40
Alignment explanation
Indices: 48077--48241 Score: 125
Period size: 40 Copynumber: 4.0 Consensus size: 40
48067 TTCCGAATTT
* * **
48077 GCAACTCGAATTTGGAATTCGCAACACAGAA-GTCGAATTC
1 GCAACTCGAATTTGAAATTCGCAACAC-GAATTTCGTTTTC
* * *
48117 GCAACTTGAATTTGACATTTTCGCAACACGAATTTCTTTTTC
1 GCAACTCGAATTTGA-A-ATTCGCAACACGAATTTCGTTTTC
* * *
48159 GCAACTCGATTTTTAAATTCGCAACACGAGTTTCGTTTTC
1 GCAACTCGAATTTGAAATTCGCAACACGAATTTCGTTTTC
** ** * * *
48199 TTAACTCGAAAAATCAAATTCGCAACTCGAATTTTCATTTTC
1 GCAACTCG-AATTTGAAATTCGCAACACGAA-TTTCGTTTTC
48241 G
1 G
48242 AGTTGGATTT
Statistics
Matches: 97, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
40 40 0.41
41 21 0.22
42 36 0.37
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (40 bp):
GCAACTCGAATTTGAAATTCGCAACACGAATTTCGTTTTC
Found at i:48253 original size:19 final size:20
Alignment explanation
Indices: 48229--48293 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
48219 CGCAACTCGA
48229 ATTTTCATTTTCGAGTTG-G
1 ATTTTCATTTTCGAGTTGCG
*
48248 ATTTTCATTTTCGAATTGCG
1 ATTTTCATTTTCGAGTTGCG
* *
48268 AATTTCATTTTCGAGTTGTG
1 ATTTTCATTTTCGAGTTGCG
48288 ATTTTC
1 ATTTTC
48294 GTGTTGCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.52
Consensus pattern (20 bp):
ATTTTCATTTTCGAGTTGCG
Found at i:48318 original size:34 final size:34
Alignment explanation
Indices: 48254--48324 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
48244 TTGGATTTTC
* *
48254 ATTTTCGAATTGCGAATTTCATTTTCGAGTTGTG
1 ATTTTCGAATTGCGAATTTCAATTTCGAGTTGCG
** *
48288 ATTTTCGTGTTGCGAATTCTGAATTT-GAGTTGCG
1 ATTTTCGAATTGCGAATT-TCAATTTCGAGTTGCG
48322 ATT
1 ATT
48325 CTGATTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (34 bp):
ATTTTCGAATTGCGAATTTCAATTTCGAGTTGCG
Found at i:55982 original size:3 final size:3
Alignment explanation
Indices: 55974--56003 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
55964 GAATTGGATT
55974 TTG TTG TTG TTG TTG TTG TTG TTG TCTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG T-TG TT
56004 ATCCTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.03, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:56914 original size:45 final size:45
Alignment explanation
Indices: 56865--56952 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
56855 GAACATCGAA
* * *
56865 TGCATTTTATGCATCGATGCACATACGATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
56910 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
56953 TGGCTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
Found at i:71131 original size:14 final size:14
Alignment explanation
Indices: 71113--71160 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 14
71103 AAAAAAATGA
71113 AAAAAAAATTGATT
1 AAAAAAAATTGATT
71127 GAAAAAAAA--GA--
1 -AAAAAAAATTGATT
71138 AAAAAAAATTGATT
1 AAAAAAAATTGATT
*
71152 CAAAAAAAT
1 AAAAAAAAT
71161 GAAGTTGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
10 8 0.29
12 2 0.07
13 2 0.07
14 8 0.29
15 8 0.29
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTGATT
Found at i:71133 original size:25 final size:25
Alignment explanation
Indices: 71101--71163 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
71091 CCACTAAAAA
71101 TGAAAAAAATGAAAAAAAAATTGAT
1 TGAAAAAAATGAAAAAAAAATTGAT
*
71126 TGAAAAAAAAGAAAAAAAAATTGAT
1 TGAAAAAAATGAAAAAAAAATTGAT
*
71151 TCAAAAAAATGAA
1 TGAAAAAAATGAA
71164 GTTGTGAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (25 bp):
TGAAAAAAATGAAAAAAAAATTGAT
Found at i:73643 original size:29 final size:30
Alignment explanation
Indices: 73611--73667 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
73601 AAACTTTGAA
73611 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
*
73640 TAAATTCAATTCAAGTCCAAAAATATTT
1 TAAATTCAATTCAAGTCCAAAAACATTT
73668 GCCATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTG
Found at i:74850 original size:27 final size:27
Alignment explanation
Indices: 74820--74878 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
74810 GCCAATCCTT
* *
74820 GGAAATATGCTAATCTCTTGTTTTCAA
1 GGAAATATGCTAATCTATTGGTTTCAA
74847 GGAAATATGCTAATCTATTGGTTTCAA
1 GGAAATATGCTAATCTATTGGTTTCAA
*
74874 AGAAA
1 GGAAA
74879 CAAAATTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (27 bp):
GGAAATATGCTAATCTATTGGTTTCAA
Found at i:75519 original size:20 final size:21
Alignment explanation
Indices: 75494--75588 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
75484 TTGTGCTTAA
75494 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
* *
75514 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAAAG
* *
75536 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAAAG
* *
75557 TGCACCGATGCACACCTTGAATG
1 TGCATCGAT--ACACCTTGAAAG
75580 TGCATCGAT
1 TGCATCGAT
75589 GCACAAGGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 13 0.21
23 20 0.33
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:75577 original size:23 final size:23
Alignment explanation
Indices: 75513--75593 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
75503 ACACCTAACA
*
75513 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
75535 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
*
75556 GTGCACCGATGCACACCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
75579 GTGCATCGATGCACA
1 GTGCATCGATGCACA
75594 AGGCCATGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.31
22 10 0.20
23 23 0.47
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:75584 original size:44 final size:42
Alignment explanation
Indices: 75494--75588 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
75484 TTGTGCTTAA
* *
75494 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAACCTTGAATG
*
75536 TGCATCGATACACCATGAA-GGTGCACCGATGCACACCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-ACCTTGAATG
75580 TGCATCGAT
1 TGCATCGAT
75589 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAACCTTGAATG
Found at i:77734 original size:13 final size:13
Alignment explanation
Indices: 77716--77744 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
77706 GGGGGAGTAA
77716 TTTCAAAATTGAT
1 TTTCAAAATTGAT
77729 TTTCAAAATTGAT
1 TTTCAAAATTGAT
77742 TTT
1 TTT
77745 TAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
TTTCAAAATTGAT
Found at i:79216 original size:21 final size:21
Alignment explanation
Indices: 79167--79208 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
79157 TAAACGATGA
* *
79167 GAGATGAATCCTGAAGAATGG
1 GAGATGGACCCTGAAGAATGG
*
79188 GAGATGGACCCTGAATAATGG
1 GAGATGGACCCTGAAGAATGG
79209 TAGGTGGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.19
Consensus pattern (21 bp):
GAGATGGACCCTGAAGAATGG
Found at i:79590 original size:21 final size:21
Alignment explanation
Indices: 79566--79673 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 21
79556 AGCACATACT
79566 TCATCACGTAAAGCACCATTG
1 TCATCACGTAAAGCACCATTG
* *
79587 TCATCACATAAAGCACCTACCACCATTA
1 TCATCACGTAAAG-------CACCATTG
*
79615 TCATCACGTAAAGCACC-TATC
1 TCATCACGTAAAGCACCAT-TG
79636 TCATCACGTAAAGCACCATTG
1 TCATCACGTAAAGCACCATTG
79657 TCATCACGTAAAGCACC
1 TCATCACGTAAAGCACC
79674 TACCTCATCA
Statistics
Matches: 73, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.01
21 52 0.71
22 1 0.01
28 19 0.26
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.22
Consensus pattern (21 bp):
TCATCACGTAAAGCACCATTG
Found at i:79618 original size:28 final size:28
Alignment explanation
Indices: 79579--79633 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
79569 TCACGTAAAG
*
79579 CACCATTGTCATCACATAAAGCACCTAC
1 CACCATTATCATCACATAAAGCACCTAC
*
79607 CACCATTATCATCACGTAAAGCACCTA
1 CACCATTATCATCACATAAAGCACCTA
79634 TCTCATCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.35, G:0.07, T:0.22
Consensus pattern (28 bp):
CACCATTATCATCACATAAAGCACCTAC
Found at i:79666 original size:42 final size:42
Alignment explanation
Indices: 79607--79694 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
79597 AAGCACCTAC
* *
79607 CACCATTATCATCACGTAAAGCACCTATCTCATCACGTAAAG
1 CACCATTATCATCACGTAAAGCACCTACCTCATCACGTAAAA
*
79649 CACCATTGTCATCACGTAAAGCACCTACCTCATCACGTAAAA
1 CACCATTATCATCACGTAAAGCACCTACCTCATCACGTAAAA
79691 CACC
1 CACC
79695 TAACTCATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.34, G:0.09, T:0.22
Consensus pattern (42 bp):
CACCATTATCATCACGTAAAGCACCTACCTCATCACGTAAAA
Found at i:79681 original size:21 final size:21
Alignment explanation
Indices: 79615--79708 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
79605 ACCACCATTA
79615 TCATCACGTAAAGCACCTATC
1 TCATCACGTAAAGCACCTATC
*
79636 TCATCACGTAAAGCACC-ATTG
1 TCATCACGTAAAGCACCTA-TC
*
79657 TCATCACGTAAAGCACCTACC
1 TCATCACGTAAAGCACCTATC
* *
79678 TCATCACGTAAAACACCTAAC
1 TCATCACGTAAAGCACCTATC
*
79699 TCATCCCGTA
1 TCATCACGTA
79709 GAGGTGAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (21 bp):
TCATCACGTAAAGCACCTATC
Found at i:79900 original size:42 final size:42
Alignment explanation
Indices: 79803--79926 Score: 175
Period size: 42 Copynumber: 3.0 Consensus size: 42
79793 ATGATGGAAT
*
79803 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCAG-T-TA-G
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTCGATG
*
79842 AGGTGATAGATCTCGGTGTCGAGGTGTAGAATCAGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTCGATG
* *
79884 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATC-GACTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCAG-CTCGATG
79926 A
1 A
79927 AAAAGTGGGG
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
39 34 0.45
40 1 0.01
41 2 0.03
42 39 0.51
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTCGATG
Found at i:85383 original size:30 final size:30
Alignment explanation
Indices: 85318--85376 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
85308 TTTAGGTTTC
* *
85318 TTTTTTATTTAATTAGATATCAAAGCTTGA
1 TTTTTTAATTAATTAGATATCAAAGATTGA
*
85348 TTTTTTAATTAATTCGATATCTAAAGATT
1 TTTTTTAATTAATTAGATATC-AAAGATT
85377 TTTTTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTTTTAATTAATTAGATATCAAAGATTGA
Found at i:91303 original size:117 final size:117
Alignment explanation
Indices: 91182--91431 Score: 392
Period size: 117 Copynumber: 2.1 Consensus size: 117
91172 TGCCCAAACA
91182 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
* * * * *
91247 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGTACCAATG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** * *
91299 AAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
* *
91364 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
*
91416 AAGTAAAGCTCGGTGC
1 AAGCAAAGCTCGGTGC
91432 GAAAGCCAAG
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (117 bp):
AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:91459 original size:117 final size:116
Alignment explanation
Indices: 91182--91493 Score: 342
Period size: 117 Copynumber: 2.7 Consensus size: 116
91172 TGCCCAAACA
* * * * *
91182 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* * * * *
91247 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGTACCAATG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** * * *
91299 AAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* *
91364 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
* * *
91416 AAGTAAAGCTCGGTG-CGAAAGCCAAG-GGCCAAGCTGAA-GAGCCGAGGGTAAATAAGCGAGAG
1 AAGCAAAGCTCGGTGAC-AAAG-CAAGTGGCCAAGC--AACAAGCCGAGGGTAAAGAAGCGAGAG
* * *
91478 CAACTGGAGTGTTTCC
62 CCATTGAAGTGTTTCC
91494 GGTGCAAAGG
Statistics
Matches: 169, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 163 0.96
118 3 0.02
119 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.15
Consensus pattern (116 bp):
AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAACAAGCCGAGGGTAAAGAAGCGAGAGCCAT
TGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:92121 original size:15 final size:15
Alignment explanation
Indices: 92101--92135 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
92091 AGCAAGGCTC
92101 TTCGAGTGAAGCTTG
1 TTCGAGTGAAGCTTG
*
92116 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
92131 TTCGA
1 TTCGA
92136 ATGGTGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:97496 original size:29 final size:29
Alignment explanation
Indices: 97464--97535 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
97454 GTGCCAAAAA
*
97464 ATAAATAACA-AAAA-TAAAAGGATAGAAAT
1 ATAAAT-ACATAAAAGT-AAAGGACAGAAAT
*
97493 ATAAATACATAAAAGTAAAGGGCAGAAAT
1 ATAAATACATAAAAGTAAAGGACAGAAAT
*
97522 ATAAATGCATAAAA
1 ATAAATACATAAAA
97536 TTAATGCTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.89
30 1 0.03
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (29 bp):
ATAAATACATAAAAGTAAAGGACAGAAAT
Found at i:97623 original size:36 final size:36
Alignment explanation
Indices: 97564--97632 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
97554 TTTGGTCGCC
*
97564 ATTTATGTCAGTTTTATTGGATCAAATT-AAAAGGAA
1 ATTTATGTCAGTTTTAATGGATC-AATTGAAAAGGAA
*
97600 ATTTATGTCATTTTTACAT-GATCAATTGAAAAG
1 ATTTATGTCAGTTTTA-ATGGATCAATTGAAAAG
97633 CAGAGCATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 4 0.14
36 24 0.83
37 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (36 bp):
ATTTATGTCAGTTTTAATGGATCAATTGAAAAGGAA
Found at i:103501 original size:65 final size:64
Alignment explanation
Indices: 103387--103585 Score: 210
Period size: 65 Copynumber: 3.1 Consensus size: 64
103377 AGTGATACAC
* * *
103387 CGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCATTTCATG
1 CGATGCACCAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGCATTTGATG
103449 CAT
62 CAT
* *
103452 TGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGC
1 CGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGC
103515 AT
63 AT
* * * * *
103517 CGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
103581 CGATG
1 CGATG
103586 TACTCTTAGT
Statistics
Matches: 114, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 45 0.39
65 61 0.54
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
CGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
Found at i:103604 original size:64 final size:63
Alignment explanation
Indices: 103429--103608 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
103419 AATTAAATTG
* * * * * *
103429 AACATCGAATGCATTTCATGCATTGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAA
* * * *
103494 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-
1 AACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGA
103557 A
63 A
*
103558 AACATCGAATGCACTTGATGCATCGATGTACTCTTAG-TGCACCGATGCACT
1 AACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
103609 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 44 0.44
65 50 0.51
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAA
Found at i:114338 original size:16 final size:16
Alignment explanation
Indices: 114317--114348 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
114307 TCATACTGAG
114317 GCTAGGGATTTAATTT
1 GCTAGGGATTTAATTT
114333 GCTAGGGATTTAATTT
1 GCTAGGGATTTAATTT
114349 CCACGATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (16 bp):
GCTAGGGATTTAATTT
Done.