Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005901.1 Hibiscus syriacus cultivar Beakdansim tig00013863_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: 86270
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6649 original size:23 final size:22
Alignment explanation
Indices: 6589--6649 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
6579 AATAAGAATA
* *
6589 ATTATGTCTTTGTGATA-TTTT
1 ATTATGTCTTTGTGACACGTTT
* *
6610 ATT-TGTCTTTATAACACGTTT
1 ATTATGTCTTTGTGACACGTTT
6631 ATTTATGTCTTTGTGACAC
1 A-TTATGTCTTTGTGACAC
6650 ATTTTTCTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 10 0.32
21 7 0.23
22 2 0.06
23 12 0.39
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.54
Consensus pattern (22 bp):
ATTATGTCTTTGTGACACGTTT
Found at i:8188 original size:21 final size:21
Alignment explanation
Indices: 8156--8197 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
8146 GATGTAAAGA
*
8156 AGTTTCAGGCAATGATTGCTG
1 AGTTTCAGGCAAGGATTGCTG
*
8177 AGTTTACA-GCAAGGGTTGCTG
1 AGTTT-CAGGCAAGGATTGCTG
8198 CATTGGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (21 bp):
AGTTTCAGGCAAGGATTGCTG
Found at i:15862 original size:31 final size:31
Alignment explanation
Indices: 15809--15897 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
15799 TAAACATAAT
*
15809 ATATTATCACTTTCA-TTTTATTTAATTAAG
1 ATATGATCACTTTCATTTTTATTTAATTAAG
* *
15839 ATATGATCACTTTTATTTTTATTTAGTTAAG
1 ATATGATCACTTTCATTTTTATTTAATTAAG
*
15870 ATATGATCACTTTCATTTTAATTTAATT
1 ATATGATCACTTTCATTTTTATTTAATT
15898 GAGGCGTGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 13 0.25
31 39 0.75
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (31 bp):
ATATGATCACTTTCATTTTTATTTAATTAAG
Found at i:16428 original size:26 final size:27
Alignment explanation
Indices: 16379--16431 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
16369 ACTTATTATG
*
16379 TATTTTATTATTAACTTAATTTTAAAA
1 TATTTTATTATTAACTTAAATTTAAAA
*
16406 TATTTTATT-TTAATTTAAATTTAAAA
1 TATTTTATTATTAACTTAAATTTAAAA
16432 ATATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTTTATTATTAACTTAAATTTAAAA
Found at i:16441 original size:56 final size:56
Alignment explanation
Indices: 16379--16560 Score: 169
Period size: 56 Copynumber: 3.2 Consensus size: 56
16369 ACTTATTATG
*
16379 TATTTTATTATTAACTTAATTTTAAAATATTTTATT-TTAATTTAAATTTAAAAATA
1 TATTTTATT-TTATCTTAATTTTAAAATATTTTATTATTAATTTAAATTTAAAAATA
* * *
16435 TATTTTATTCTTATCTAAATTTTTAAAAATATATTTTATTATTATTTTAACTTTAGAAAATA
1 TATTTTATT-TTATCTTAA-TTTT--AAA-ATATTTTATTATTAATTTAAATTTA-AAAATA
* *
16497 TA---TATTTTATCTTAA-TTTACTAAATATTCATATTATTACTTTAAA-TTAATAAATA
1 TATTTTATTTTATCTTAATTTTA--AAATATT-TTATTATTAATTTAAATTTAA-AAATA
16552 TATTTTATT
1 TATTTTATT
16561 CTCATTACAA
Statistics
Matches: 104, Mismatches: 9, Indels: 24
0.76 0.07 0.18
Matches are distributed among these distances:
54 2 0.02
55 15 0.14
56 34 0.33
57 4 0.04
58 12 0.12
59 7 0.07
60 10 0.10
61 12 0.12
62 8 0.08
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (56 bp):
TATTTTATTTTATCTTAATTTTAAAATATTTTATTATTAATTTAAATTTAAAAATA
Found at i:16463 original size:31 final size:31
Alignment explanation
Indices: 16405--16515 Score: 113
Period size: 31 Copynumber: 3.6 Consensus size: 31
16395 TAATTTTAAA
16405 ATATTTTATT-TTAATTTAAA--TTTAAAAAT
1 ATATTTTATTCTT-ATTTAAATTTTTAAAAAT
*
16434 ATATTTTATTCTTATCTAAATTTTTAAAAAT
1 ATATTTTATTCTTATTTAAATTTTTAAAAAT
* * **
16465 ATATTTTATTATTATTTTAACTTTAGAAAATAT
1 ATATTTTATTCTTA-TTTAAATTTTTAAAA-AT
16498 ATATTTTA-TCTTAATTTA
1 ATATTTTATTCTT-ATTTA
16516 CTAAATATTC
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
29 16 0.23
30 2 0.03
31 22 0.32
32 18 0.26
33 11 0.16
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.56
Consensus pattern (31 bp):
ATATTTTATTCTTATTTAAATTTTTAAAAAT
Found at i:16521 original size:26 final size:27
Alignment explanation
Indices: 16492--16560 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
16482 TAACTTTAGA
* *
16492 AAATATATATT-TTA-TCTTAATTTACT
1 AAATATATATTATTACT-TTAAATTAAT
16518 AAATATTCATATTATTACTTTAAATTAAT
1 AAATA-T-ATATTATTACTTTAAATTAAT
*
16547 AAATATATTTTATT
1 AAATATATATTATT
16561 CTCATTACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.14
27 8 0.22
28 6 0.17
29 16 0.44
30 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATATATATTATTACTTTAAATTAAT
Found at i:17171 original size:21 final size:21
Alignment explanation
Indices: 17093--17172 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
17083 AAATCAGTTC
* *
17093 CCAGAATCGCAACGCGACTAT
1 CCAGAATCGCAATGCGATTAT
**
17114 GAAGAATCGCAATGCGA-TAGT
1 CCAGAATCGCAATGCGATTA-T
* * * *
17135 ACA-AATTAGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATTAT
17156 CCAGAATCGCAATGCGA
1 CCAGAATCGCAATGCGA
17173 ATATGAAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 4 0.09
21 37 0.84
22 3 0.07
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
CCAGAATCGCAATGCGATTAT
Found at i:17266 original size:41 final size:41
Alignment explanation
Indices: 17221--17406 Score: 268
Period size: 40 Copynumber: 4.6 Consensus size: 41
17211 GATTCTGACT
* * *
17221 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
17262 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
17303 ATTGCAACGAGAATACGT-AAATCGCAACGCATATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
17343 ATCGCAATGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
17383 ATCGCAACGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATC
17407 ACAATGCGAT
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 71 0.55
41 58 0.45
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:17269 original size:20 final size:20
Alignment explanation
Indices: 17221--17391 Score: 173
Period size: 20 Copynumber: 8.4 Consensus size: 20
17211 GATTCTGACT
*
17221 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
17242 ATCACAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
17262 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
17283 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
17303 ATTGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
17323 ATCGCAACGCATATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
17343 ATCGCAATGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
17363 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
17383 ATCGCAACG
1 ATCGCAACG
17392 ACAATACGTA
Statistics
Matches: 120, Mismatches: 27, Indels: 7
0.78 0.18 0.05
Matches are distributed among these distances:
20 87 0.73
21 33 0.28
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:17436 original size:80 final size:81
Alignment explanation
Indices: 17221--17436 Score: 240
Period size: 80 Copynumber: 2.7 Consensus size: 81
17211 GATTCTGACT
** * * * * * *
17221 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGACAATACGT-AAATCACAACGCATATCTGTAAAGCGCAATGAGAATACGTAAAATC
17286 GCAACGCGTATCCGTAA
65 GCAACGCGTATCCGTAA
* * * *
17303 ATTGCAACGAGAATACGTAAATCGCAACGCATATCTGTAAATCGCAATGAGAATACGT-AAATCG
1 ATCGCAACGACAATACGTAAATCACAACGCATATCTGTAAAGCGCAATGAGAATACGTAAAATCG
*
17367 CAATGCGTATCCGTAA
66 CAACGCGTATCCGTAA
* * *
17383 ATCGCAACGACAATACGTAAAATCACAATGCGATAT-T-TAAAGCGCCATTAGAAT
1 ATCGCAACGACAATACGT-AAATCACAACGC-ATATCTGTAAAGCGCAATGAGAAT
17437 CGCTACGCGT
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
80 51 0.44
81 46 0.40
82 19 0.16
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (81 bp):
ATCGCAACGACAATACGTAAATCACAACGCATATCTGTAAAGCGCAATGAGAATACGTAAAATCG
CAACGCGTATCCGTAA
Found at i:18033 original size:21 final size:21
Alignment explanation
Indices: 17972--18064 Score: 106
Period size: 20 Copynumber: 4.6 Consensus size: 21
17962 TTCTAAACTT
*
17972 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGACGAAAATG
17992 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
18012 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
18033 AAAATCGCAACG-CG-AAATG
1 AAAATCGCAACGACGAAAATG
*
18052 AAAATTGCAACGA
1 AAAATCGCAACGA
18065 GATAATCGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.25
20 30 0.48
21 17 0.27
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:18051 original size:40 final size:40
Alignment explanation
Indices: 17972--18066 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
17962 TTCTAAACTT
17972 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** *
18012 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
*
18052 AAAATTGCAACGAGA
1 AAAATCGCAACGAGA
18067 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.51, C:0.18, G:0.19, T:0.13
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:18142 original size:33 final size:33
Alignment explanation
Indices: 18094--18175 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
18084 CAAAATCGCA
18094 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
18127 TTGTGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
18160 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
18176 AACCAAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:18296 original size:25 final size:24
Alignment explanation
Indices: 18242--18296 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
18232 TTATGTTTAT
* *
18242 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
18266 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
18292 TGTTT
1 TGTTT
18297 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:20026 original size:94 final size:94
Alignment explanation
Indices: 19865--20244 Score: 602
Period size: 94 Copynumber: 4.1 Consensus size: 94
19855 TAGATTGCTT
* *
19865 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
19930 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
19959 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACCGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
20024 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
20053 AGTAAATTTGTTCGATTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
20118 ATTTGTCTTTGTTTAGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * ** * *
20147 AGTAAATTTGTTCAGTTGCTGTTAATTCTGCTAAACTGTGTATTCTTTAATACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
20212 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
20240 AGTAA
1 AGTAA
20245 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
93 26 0.10
94 240 0.90
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:20345 original size:19 final size:19
Alignment explanation
Indices: 20306--20424 Score: 113
Period size: 19 Copynumber: 6.4 Consensus size: 19
20296 CACGAAACTT
*
20306 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GCAAAATG
**
20327 ATTATCGCAACGCAAAATG
1 AAAATCGCAACGCAAAATG
*
20346 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCAAAATG
*
20365 AAAATCGCAATGCAAAATG
1 AAAATCGCAACGCAAAATG
*
20384 AAAATCGTAACG----A-G
1 AAAATCGCAACGCAAAATG
* *
20398 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCAAAATG
20417 AAAATCGC
1 AAAATCGC
20425 GTTGTCATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
18 1 0.01
19 58 0.73
21 9 0.11
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCAAAATG
Found at i:20847 original size:21 final size:21
Alignment explanation
Indices: 20823--20889 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20813 TCATTACTCG
20823 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
20844 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
20865 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
20886 AGAG
1 AGAG
20890 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:22260 original size:14 final size:13
Alignment explanation
Indices: 22241--22276 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
22231 ATTGTTTAAT
22241 TGATTTGTAAAAG
1 TGATTTGTAAAAG
22254 ATGATTTGTAAAAG
1 -TGATTTGTAAAAG
22268 TGAATTTGT
1 TG-ATTTGT
22277 TTTATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (13 bp):
TGATTTGTAAAAG
Found at i:22399 original size:19 final size:19
Alignment explanation
Indices: 22383--22478 Score: 123
Period size: 19 Copynumber: 5.3 Consensus size: 19
22373 AAAAATGACT
22383 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22402 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
22421 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22440 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
*
22454 ATCGCAACGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
22473 ATCGCA
1 ATCGCA
22479 GCGCGAAACT
Statistics
Matches: 71, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
14 10 0.14
15 2 0.03
16 2 0.03
17 2 0.03
18 1 0.01
19 54 0.76
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:22460 original size:33 final size:36
Alignment explanation
Indices: 22383--22478 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 36
22373 AAAAATGACT
*
22383 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAA-GCG-AATGAAA
22421 ATCGCAACGCGAAATGAAAATCGCAA-CG-AT-AAA
1 ATCGCAACGCGAAATGAAAATCGCAAGCGAATGAAA
22454 ATCGCAACGCGAAACT-AAAATCGCA
1 ATCGCAACGCGAAA-TGAAAATCGCA
22479 GCGCGAAACT
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
33 26 0.46
34 3 0.05
36 2 0.04
38 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:22483 original size:19 final size:19
Alignment explanation
Indices: 22383--22496 Score: 109
Period size: 19 Copynumber: 6.3 Consensus size: 19
22373 AAAAATGACT
*
22383 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
*
22402 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
22421 ATCGCAACGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
22440 ATCGCAA--CG--A-TAAA
1 ATCGCAACGCGAAACTAAA
22454 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
22473 ATCGCAGCGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
22492 TTCGC
1 ATCGC
22497 GTTGTGATTT
Statistics
Matches: 87, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.11
15 2 0.02
16 2 0.02
17 2 0.02
18 1 0.01
19 70 0.80
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:22514 original size:19 final size:19
Alignment explanation
Indices: 22492--22630 Score: 100
Period size: 19 Copynumber: 7.7 Consensus size: 19
22482 CGAAACTAAA
*
22492 TTCGCGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22511 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
22526 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
22544 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
22563 TTCTGCGTTGCGATATTCAT
1 TTC-GCGTTGCGATTTTCAT
*
22583 ATTTGCGTTGCGATTTTCA-
1 -TTCGCGTTGCGATTTTCAT
*
22602 ----CGTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22617 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
22631 ATCTCGTTGC
Statistics
Matches: 93, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
14 22 0.24
16 3 0.03
17 3 0.03
19 35 0.38
20 28 0.30
21 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:22539 original size:33 final size:33
Alignment explanation
Indices: 22496--22643 Score: 152
Period size: 33 Copynumber: 4.3 Consensus size: 33
22486 ACTAAATTCG
* *
22496 CGTTGTGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
22529 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---TCT
* * * * *
22567 GCGTTGCGATATTCATATTTGCGTTGCGATTTTCA
1 -CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
* *
22602 CGTTACGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
22635 CGTTGCGAT
1 CGTTGCGAT
22644 AGTAATTTCC
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
33 48 0.51
34 13 0.14
35 4 0.04
38 4 0.04
39 14 0.15
40 11 0.12
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:22575 original size:20 final size:20
Alignment explanation
Indices: 22529--22601 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
22519 GCGATTCTCT
*
22529 CGTTGCGATTTTCATTTC-G
1 CGTTGCGATATTCATTTCTG
* *
22548 CATTGCGATAGTCATTTCTG
1 CGTTGCGATATTCATTTCTG
22568 CGTTGCGATATTCATATT-TG
1 CGTTGCGATATTCAT-TTCTG
*
22588 CGTTGCGATTTTCA
1 CGTTGCGATATTCA
22602 CGTTACGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.33
20 29 0.63
21 2 0.04
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (20 bp):
CGTTGCGATATTCATTTCTG
Found at i:24993 original size:6 final size:6
Alignment explanation
Indices: 24982--25044 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
24972 CTTTGGGGAT
* * * *
24982 TTCTTC TTCTTC TTCTTC TTCTTT TTCTTC TTATTC TTTTTC TTCTTA
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
*
25030 TTCTTT TTCTTC TTC
1 TTCTTC TTCTTC TTC
25045 AGTGTTATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (6 bp):
TTCTTC
Found at i:24996 original size:9 final size:9
Alignment explanation
Indices: 24982--25044 Score: 81
Period size: 9 Copynumber: 7.0 Consensus size: 9
24972 CTTTGGGGAT
24982 TTCTTCTTC
1 TTCTTCTTC
24991 TTCTTCTTC
1 TTCTTCTTC
*
25000 TTCTTTTTC
1 TTCTTCTTC
*
25009 TTCTTATTC
1 TTCTTCTTC
*
25018 TTTTTCTTC
1 TTCTTCTTC
* *
25027 TTATTCTTT
1 TTCTTCTTC
25036 TTCTTCTTC
1 TTCTTCTTC
25045 AGTGTTATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (9 bp):
TTCTTCTTC
Found at i:25000 original size:15 final size:15
Alignment explanation
Indices: 24982--25044 Score: 99
Period size: 15 Copynumber: 4.2 Consensus size: 15
24972 CTTTGGGGAT
*
24982 TTCTTCTTCTTCTTC
1 TTCTTCTTTTTCTTC
24997 TTCTTCTTTTTCTTC
1 TTCTTCTTTTTCTTC
*
25012 TTATTCTTTTTCTTC
1 TTCTTCTTTTTCTTC
*
25027 TTATTCTTTTTCTTC
1 TTCTTCTTTTTCTTC
25042 TTC
1 TTC
25045 AGTGTTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTCTTTTTCTTC
Found at i:25253 original size:24 final size:24
Alignment explanation
Indices: 25219--25272 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
25209 CTGAAAAATT
25219 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
25243 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
25267 ATCAAA
1 ATCAAA
25273 TTTCGAATAC
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:26166 original size:21 final size:21
Alignment explanation
Indices: 26132--26222 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
26122 GTCAGAATCT
26132 CGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTTACGGATACG
* *
26152 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGATTTTACGGATACG
26172 TCGTTGCGA-TTTACGGATACG
1 -CGTTGCGATTTTACGGATACG
* *
26193 CGTTGTGATTTTACGGATACT
1 CGTTGCGATTTTACGGATACG
*
26214 TGTTGCGAT
1 CGTTGCGAT
26223 AGTCAGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 24 0.41
21 35 0.59
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTTACGGATACG
Found at i:26219 original size:41 final size:41
Alignment explanation
Indices: 26130--26222 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
26120 TAGTCAGAAT
* *
26130 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT
1 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
* *
26171 GTCGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATA
1 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
*
26212 CTTGTTGCGAT
1 CTCGTTGCGAT
26223 AGTCAGAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (41 bp):
CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
Found at i:26285 original size:20 final size:21
Alignment explanation
Indices: 26231--26285 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
26221 ATAGTCAGAA
26231 TCGCGTTGCGA-TTTATATGT
1 TCGCGTTGCGATTTTATATGT
26251 TCGCGTTGCGATTTTCATAT-T
1 TCGCGTTGCGATTTT-ATATGT
26272 T-GCGTTGCGATTTT
1 TCGCGTTGCGATTTT
26286 GGAAAATCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 24 0.73
21 5 0.15
22 4 0.12
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (21 bp):
TCGCGTTGCGATTTTATATGT
Found at i:26836 original size:45 final size:45
Alignment explanation
Indices: 26781--26870 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
26771 AATTAAAATT
26781 GAATTTATAAATTTGTTAAATGACTTCAACTATATTTTAAATGTG
1 GAATTTATAAATTTGTTAAATGACTTCAACTATATTTTAAATGTG
*
26826 GAATTTATAAATTTGTTAATTGACTTCAACTATATTTTAAATGTG
1 GAATTTATAAATTTGTTAAATGACTTCAACTATATTTTAAATGTG
26871 TCGTGAACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (45 bp):
GAATTTATAAATTTGTTAAATGACTTCAACTATATTTTAAATGTG
Found at i:26862 original size:23 final size:23
Alignment explanation
Indices: 26791--26862 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
26781 GAATTTATAA
*
26791 ATTTGTTAAATGACTTCAACTAT
1 ATTTGTTAATTGACTTCAACTAT
* * * *
26814 ATTT-TAAATGTGGAATT-TA-TAA
1 ATTTGTTAAT-T-GACTTCAACTAT
26836 ATTTGTTAATTGACTTCAACTAT
1 ATTTGTTAATTGACTTCAACTAT
26859 ATTT
1 ATTT
26863 TAAATGTGTC
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 16 0.46
24 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (23 bp):
ATTTGTTAATTGACTTCAACTAT
Found at i:27450 original size:7 final size:7
Alignment explanation
Indices: 27432--27470 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
27422 CCGAAAGAAC
27432 ATATATTT
1 ATATA-TT
27440 ATATATT
1 ATATATT
27447 ATATATT
1 ATATATT
*
27454 ACATA-T
1 ATATATT
27460 ATATATT
1 ATATATT
27467 ATAT
1 ATAT
27471 CAATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 5 0.18
7 18 0.64
8 5 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATATT
Found at i:27476 original size:13 final size:13
Alignment explanation
Indices: 27432--27470 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
27422 CCGAAAGAAC
27432 ATATAT-TTATAT
1 ATATATATTATAT
*
27444 ATTATATATTACAT
1 A-TATATATTATAT
27458 ATATATATTATAT
1 ATATATATTATAT
27471 CAATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 1 0.04
13 16 0.70
14 6 0.26
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:27476 original size:24 final size:24
Alignment explanation
Indices: 27430--27478 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
27420 GACCGAAAGA
* *
27430 ACATATATTTATATATTATATATT
1 ACATATATATATATATCATATATT
27454 ACATATATATATTATATCA-ATATT
1 ACATATATATA-TATATCATATATT
27478 A
1 A
27479 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (24 bp):
ACATATATATATATATCATATATT
Found at i:28623 original size:24 final size:24
Alignment explanation
Indices: 28596--28644 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
28586 TTTTTCTTAA
28596 TATTTT-ATTTATTTATATTACTAT
1 TATTTTCATTTATTTATATT-CTAT
*
28620 TATTTTCTTTTATTTATATTCTAT
1 TATTTTCATTTATTTATATTCTAT
28644 T
1 T
28645 TCTATTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTCATTTATTTATATTCTAT
Found at i:28933 original size:19 final size:19
Alignment explanation
Indices: 28911--28960 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
28901 ACCAAACCTT
28911 TATCCTTTTTTCAAA-TCTG
1 TATCCTTTTTTCAAATTC-G
*
28930 TATCCTTTTTTTAAATTCG
1 TATCCTTTTTTCAAATTCG
*
28949 TATCCCTTTTTC
1 TATCCTTTTTTC
28961 TATTTTCGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (19 bp):
TATCCTTTTTTCAAATTCG
Found at i:29167 original size:17 final size:17
Alignment explanation
Indices: 29145--29178 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29135 TGTGTTTGTT
29145 TTTATTT-TATTATCTTA
1 TTTATTTAT-TTATCTTA
29162 TTTATTTATTTATCTTA
1 TTTATTTATTTATCTTA
29179 GCTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTATTTATCTTA
Found at i:37825 original size:21 final size:21
Alignment explanation
Indices: 37800--37847 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
37790 CTAAATTGAG
37800 AAAAGGAA-AAAAAAAGAGGAA
1 AAAAGGAATAAAAAAAGA-GAA
*
37821 AAAA-GAATAAAAGAAGAGAA
1 AAAAGGAATAAAAAAAGAGAA
37841 AATAAGG
1 AA-AAGG
37848 TGGGTTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 8 0.35
21 14 0.61
22 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (21 bp):
AAAAGGAATAAAAAAAGAGAA
Found at i:38752 original size:94 final size:94
Alignment explanation
Indices: 38591--39272 Score: 959
Period size: 94 Copynumber: 7.1 Consensus size: 94
38581 TTACCCAGAG
38591 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
38656 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
* *** *
38685 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCAAGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
** ***
38750 GGGACCGCTGACTGTCAACTTCTCAATTTC
66 GGGACCGCTGGTTGTCAA-TAAACAATTTC
38780 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
38845 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
62 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
* *** *
38878 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCAAGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
** ***
38943 GGGACCGCTGACTGTCAACTTCTCAATTTC
66 GGGACCGCTGGTTGTCAA-TAAACAATTTC
38973 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
39038 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
62 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
* *** *
39071 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCAAGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* ** * *
39136 GGGATCGCTGACTGTCAACTTATCAATTTC
66 GGGACCGCTGGTTGTCAA-TAAACAATTTC
39166 AAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
39231 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
62 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
39264 CCAATTTCA
1 CCAATTTCA
39273 GCTAGAAGAC
Statistics
Matches: 513, Mismatches: 60, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
94 236 0.46
95 25 0.05
98 25 0.05
99 227 0.44
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:38915 original size:193 final size:193
Alignment explanation
Indices: 38586--39272 Score: 1347
Period size: 193 Copynumber: 3.6 Consensus size: 193
38576 AGGTTTTACC
38586 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38651 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
38716 ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
131 ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
38779 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38844 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
38909 ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
131 ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
38972 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39037 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
* *
39102 ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGATCGCTGACTGTCAACTTATCAATTT
131 ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
*
39165 CAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39230 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
39273 GCTAGAAGAC
Statistics
Matches: 491, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 491 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (193 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
ACTCAAGACAGTACAAGTTCAACTTCAAGACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
Found at i:39334 original size:20 final size:20
Alignment explanation
Indices: 39309--39350 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39299 CCAGAACTCT
39309 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
39329 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
39349 GA
1 GA
39351 CGAAGGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:39597 original size:7 final size:7
Alignment explanation
Indices: 39579--39617 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
39569 CCGAAAGAAC
39579 ATATATTT
1 ATATA-TT
39587 ATATATT
1 ATATATT
39594 ATATATT
1 ATATATT
*
39601 ACATA-T
1 ATATATT
39607 ATATATT
1 ATATATT
39614 ATAT
1 ATAT
39618 CAATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 5 0.18
7 18 0.64
8 5 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATATT
Found at i:39605 original size:24 final size:24
Alignment explanation
Indices: 39577--39625 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
39567 GACCGAAAGA
* *
39577 ACATATATTTA-TATATTATATATT
1 ACATATATATATTATATCA-ATATT
39601 ACATATATATATTATATCAATATT
1 ACATATATATATTATATCAATATT
39625 A
1 A
39626 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (24 bp):
ACATATATATATTATATCAATATT
Found at i:39623 original size:13 final size:13
Alignment explanation
Indices: 39579--39617 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
39569 CCGAAAGAAC
39579 ATATAT-TTATAT
1 ATATATATTATAT
*
39591 ATTATATATTACAT
1 A-TATATATTATAT
39605 ATATATATTATAT
1 ATATATATTATAT
39618 CAATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 1 0.04
13 16 0.70
14 6 0.26
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:40792 original size:24 final size:24
Alignment explanation
Indices: 40765--40813 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
40755 TTTTTCTTAA
40765 TATTTT-ATTTATTTATATTACTAT
1 TATTTTCATTTATTTATATT-CTAT
*
40789 TATTTTCTTTTATTTATATTCTAT
1 TATTTTCATTTATTTATATTCTAT
40813 T
1 T
40814 TCTATTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTCATTTATTTATATTCTAT
Found at i:41102 original size:19 final size:19
Alignment explanation
Indices: 41080--41129 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
41070 ACCAAACCTT
41080 TATCCTTTTTTCAAA-TCTG
1 TATCCTTTTTTCAAATTC-G
*
41099 TATCCTTTTTTTAAATTCG
1 TATCCTTTTTTCAAATTCG
*
41118 TATCCCTTTTTC
1 TATCCTTTTTTC
41130 TATTTTCGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (19 bp):
TATCCTTTTTTCAAATTCG
Found at i:41333 original size:17 final size:17
Alignment explanation
Indices: 41311--41344 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41301 TGTGTTTGTT
41311 TTTATTT-TATTATCTTA
1 TTTATTTAT-TTATCTTA
41328 TTTATTTATTTATCTTA
1 TTTATTTATTTATCTTA
41345 GCTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTATTTATCTTA
Found at i:45406 original size:2 final size:2
Alignment explanation
Indices: 45399--45429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45389 TCTTTTATCG
45399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45430 GTTAATCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49705 original size:124 final size:123
Alignment explanation
Indices: 49494--49716 Score: 333
Period size: 124 Copynumber: 1.8 Consensus size: 123
49484 AAAATAAATT
* * *
49494 AAGTTCCAAAGGTTAAAGTAAATGCAAGCAAGGTAATCCATGGAAACTGCCTCGACAGTATGATG
1 AAGTTCCAAAGGTTAAACTAAATACAAGCAAGGTAATCCATGGAAACTGCCTCGACAGAATGATG
* *
49559 TGGTTTAAGACCACTGTGAACAATTTTAGGAGTACACTCTCCGTGCCAATAATAACCG
66 TGGTTTAAGACCAATGCGAACAATTTTAGGAGTACACTCTCCGTGCCAATAATAACCG
* *
49617 AAGTTCCAAAGGTTAAACTACAATACATA-CAAGGTAATCCA-GAGAGACTGCCTCTACAGAATG
1 AAGTTCCAAAGGTTAAACTA-AATACA-AGCAAGGTAATCCATG-GAAACTGCCTCGACAGAATG
*
49680 GTGTGGTTTAAGACCAATGCGAACAATTTTAGGAGTA
63 ATGTGGTTTAAGACCAATGCGAACAATTTTAGGAGTA
49717 TATGCACGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
123 20 0.22
124 68 0.76
125 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (123 bp):
AAGTTCCAAAGGTTAAACTAAATACAAGCAAGGTAATCCATGGAAACTGCCTCGACAGAATGATG
TGGTTTAAGACCAATGCGAACAATTTTAGGAGTACACTCTCCGTGCCAATAATAACCG
Found at i:60123 original size:30 final size:32
Alignment explanation
Indices: 60063--60130 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
60053 AAATACATAT
**
60063 GATATGATCAATTTCGTTTTTGTTTAATT-AA
1 GATATGATCAATTTCGTTTTTACTTAATTAAA
*
60094 GATATGAT-AATTTTTGTTTTTACTT-ATTAAA
1 GATATGATCAA-TTTCGTTTTTACTTAATTAAA
60125 GATATG
1 GATATG
60131 GTCACCACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (32 bp):
GATATGATCAATTTCGTTTTTACTTAATTAAA
Found at i:64170 original size:35 final size:35
Alignment explanation
Indices: 64102--64171 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
64092 CAATGACTTA
***
64102 CTTTGTTTTTATGCCATTAATTCACTCGTAATCAC
1 CTTTGTTTTTATGCCATTAATTCACTAAAAATCAC
*
64137 CTTT-TTTTTCATGCCATTAATTCTCTAAAAATCAC
1 CTTTGTTTTT-ATGCCATTAATTCACTAAAAATCAC
64172 TCAGTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.46
Consensus pattern (35 bp):
CTTTGTTTTTATGCCATTAATTCACTAAAAATCAC
Found at i:64415 original size:2 final size:2
Alignment explanation
Indices: 64410--64445 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
64400 AAATAAAATA
64410 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
64446 TTATTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65145 original size:54 final size:54
Alignment explanation
Indices: 65081--65188 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
65071 AAACAGTACA
* *
65081 GTGAAGAGTGTTCATGTAAT-AATTTTTCGATTTAAAGACGATGAATCAAAATCG
1 GTGAAGAGTGTTCATATAATAAATATTT-GATTTAAAGACGATGAATCAAAATCG
*
65135 GTGAAGAGTGTTCATATGATAAATATTTGATTTAAAGACGATGAATCAAAATCG
1 GTGAAGAGTGTTCATATAATAAATATTTGATTTAAAGACGATGAATCAAAATCG
65189 CATCCGAATC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 44 0.88
55 6 0.12
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (54 bp):
GTGAAGAGTGTTCATATAATAAATATTTGATTTAAAGACGATGAATCAAAATCG
Found at i:69250 original size:67 final size:67
Alignment explanation
Indices: 69106--69254 Score: 174
Period size: 67 Copynumber: 2.2 Consensus size: 67
69096 AAAAATTTGT
* * * *
69106 TGCTCGTTAAACTCGTTAAAATTTTGCTCAACTTGTGCTCGTTAAGAAAATTTGTTGCTAAACTC
1 TGCTCGTTAAGCTCATTAAAATTTTACTCAACTTGTGCTCGTTAAGAAAATTTGTTACTAAACTC
**
69171 TT
66 GC
* * * **
69173 TACTCGTTAAGCTCATTAAAATTTTACTCGAA-TTGTGCTTGTTAAGAAAATTTGTTATTCGACT
1 TGCTCGTTAAGCTCATTAAAATTTTACTC-AACTTGTGCTCGTTAAGAAAATTTGTTACTAAACT
69237 CGC
65 CGC
*
69240 TGCTCATTAAGCTCA
1 TGCTCGTTAAGCTCA
69255 CTGCTCGTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 66 0.97
68 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (67 bp):
TGCTCGTTAAGCTCATTAAAATTTTACTCAACTTGTGCTCGTTAAGAAAATTTGTTACTAAACTC
GC
Found at i:84696 original size:53 final size:57
Alignment explanation
Indices: 84614--84731 Score: 124
Period size: 57 Copynumber: 2.1 Consensus size: 57
84604 TAAAGTCACA
*
84614 AAAAG-TATATAAATGAGTCCCAGATTAT-AAG-ATTT-TTCAGTCTATT-GACTATT
1 AAAAGTTATATAAATGAGTCCCAGACTATAAAGTATTTGTTCAGTC-ATTCGACTATT
* * *
84667 AAAAGTTATA-AAATG-GTCCCTTGACTATAAAGTTTTTTGTTGAGTCATTCGACTATT
1 AAAAGTTATATAAATGAGTCCC-AGACTATAAAG-TATTTGTTCAGTCATTCGACTATT
84724 AAAAGTTA
1 AAAAGTTA
84732 CAAATGATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
52 5 0.09
53 15 0.28
54 7 0.13
56 6 0.11
57 21 0.39
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (57 bp):
AAAAGTTATATAAATGAGTCCCAGACTATAAAGTATTTGTTCAGTCATTCGACTATT
Done.