Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004807.1 Hibiscus syriacus cultivar Beakdansim tig00010827_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: 60424
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:16622 original size:40 final size:39
Alignment explanation
Indices: 16563--16674 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 39
16553 TATTGTGAAT
* *
16563 AAATACATTT-TTAACCTAATGAATATAATTAATATAGAA
1 AAATAAATTTATTAATCTAATGAATATAATTAATATAG-A
*
16602 AAATAAATTTATTAATCTAATG-GTCATAATTAATATAGA
1 AAATAAATTTATTAATCTAATGAAT-ATAATTAATATAGA
*
16641 AAATAAAATTTATTAATCTAA-CAATTATAATTAA
1 AAAT-AAATTTATTAATCTAATGAA-TATAATTAA
16675 ATTTATTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
39 15 0.24
40 47 0.75
41 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (39 bp):
AAATAAATTTATTAATCTAATGAATATAATTAATATAGA
Found at i:16676 original size:27 final size:27
Alignment explanation
Indices: 16646--16701 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
16636 ATAGAAAATA
16646 AAATTTATTAATCTAACAATTATAATT
1 AAATTTATTAATCTAACAATTATAATT
**
16673 AAATTTATTAATCTAATGATTATAATT
1 AAATTTATTAATCTAACAATTATAATT
16700 AA
1 AA
16702 TAAAAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (27 bp):
AAATTTATTAATCTAACAATTATAATT
Found at i:17484 original size:2 final size:2
Alignment explanation
Indices: 17449--17476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17439 CACATTACTT
17449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17477 AAATATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19196 original size:2 final size:2
Alignment explanation
Indices: 19189--19221 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19179 GCTCCATTGT
19189 TA 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 TA T
19222 TGACGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29287 original size:20 final size:20
Alignment explanation
Indices: 29262--29314 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
29252 GACCAACAAA
29262 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
29282 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
29302 TTCGCAACGCGAA
1 TTCGCAACGCGAA
29315 TTTGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:29350 original size:40 final size:41
Alignment explanation
Indices: 29306--29409 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 41
29296 TCCAATTTCG
29306 CAACGCGAATTTGT-AAA-TCGCAACACAAAAGTCAAATTCC
1 CAACGCGAATTTGTCAAATTCGCAACAC-AAAGTCAAATTCC
* * *
29346 CAACGTG-A-TAGTCAAATTCGCAACACAAAGTCAAATTCG
1 CAACGCGAATTTGTCAAATTCGCAACACAAAGTCAAATTCC
29385 CAACGCGGAA-TT-TCAAATTCGCAAC
1 CAACGC-GAATTTGTCAAATTCGCAAC
29410 TGAATTTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
38 3 0.05
39 21 0.38
40 29 0.53
41 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.20
Consensus pattern (41 bp):
CAACGCGAATTTGTCAAATTCGCAACACAAAGTCAAATTCC
Found at i:29379 original size:19 final size:19
Alignment explanation
Indices: 29323--29429 Score: 79
Period size: 19 Copynumber: 5.4 Consensus size: 19
29313 AATTTGTAAA
29323 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-AAAGTCAAAT
* ** *
29343 TCCCAACGTGATAGTCAAAT
1 TCGCAAC-ACAAAGTCAAAT
29363 TCGCAACACAAAGTCAAAT
1 TCGCAACACAAAGTCAAAT
* **
29382 TCGCAACGCGGAATTTCAAAT
1 TCGCAACAC--AAAGTCAAAT
** **
29403 TCGCAACTGAATTTCAAAT
1 TCGCAACACAAAGTCAAAT
29422 TCGCAACA
1 TCGCAACA
29430 GGTTTTAGTT
Statistics
Matches: 70, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
19 34 0.49
20 21 0.30
21 15 0.21
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (19 bp):
TCGCAACACAAAGTCAAAT
Found at i:29402 original size:21 final size:20
Alignment explanation
Indices: 29376--29428 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
29366 CAACACAAAG
29376 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAAC-CGGAATT
*
29397 TCAAATTCGCAA-CTGAATT
1 TCAAATTCGCAACCGGAATT
29416 TCAAATTCGCAAC
1 TCAAATTCGCAAC
29429 AGGTTTTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (20 bp):
TCAAATTCGCAACCGGAATT
Found at i:29604 original size:14 final size:15
Alignment explanation
Indices: 29585--29622 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29575 TCCCCATCTC
29585 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
29599 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
29615 TAATTTTT
1 TAATTTTT
29623 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:32635 original size:18 final size:18
Alignment explanation
Indices: 32612--32647 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
32602 AAGCAAAAGG
*
32612 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
32630 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
32648 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:32962 original size:20 final size:20
Alignment explanation
Indices: 32937--32975 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
32927 TGCGATCAAC
32937 GCGAAAGTCAAATTCGCAAT
1 GCGAAAGTCAAATTCGCAAT
32957 GCGAAAGTCAAATTCGCAA
1 GCGAAAGTCAAATTCGCAA
32976 ACTAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAT
Found at i:33263 original size:30 final size:29
Alignment explanation
Indices: 33227--33284 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
33217 TTTCATTTAG
33227 ATGAGATGGGATGTGTATAACAAAACAATT
1 ATGAGATGGGATGTGTATAA-AAAACAATT
*
33257 ATGAGATGGGTTGTGTATAAAAAACAAT
1 ATGAGATGGGATGTGTATAAAAAACAAT
33285 CTATCTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.28
Consensus pattern (29 bp):
ATGAGATGGGATGTGTATAAAAAACAATT
Found at i:33499 original size:24 final size:25
Alignment explanation
Indices: 33472--33526 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
33462 ATTCAAATTC
*
33472 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
33496 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
33520 ATTTCAA
1 ATTTCAA
33527 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:33512 original size:18 final size:18
Alignment explanation
Indices: 33491--33527 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33481 GTAATTGGAG
33491 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
33509 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
33527 T
1 T
33528 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:33534 original size:24 final size:24
Alignment explanation
Indices: 33483--33535 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
33473 TTTCATATGT
* * *
33483 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
33507 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
33531 AATTT
1 AATTT
33536 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:33880 original size:39 final size:39
Alignment explanation
Indices: 33837--33923 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
33827 TCCGATGTTC
*
33837 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
*
33876 ATCAAAATCCAAATCTCATATAGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
33915 ATCAAAATC
1 ATCAAAATC
33924 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATAGTGCCAAGCAAAAGGAA
Found at i:34373 original size:66 final size:60
Alignment explanation
Indices: 34293--34432 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 60
34283 TTTTAGAAAC
*
34293 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACACATC-AATT
34358 A
60 A
* * *
34359 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
34419 AACAAATCAACTTT
1 AACAAATCAACTTT
34433 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 19 0.27
61 22 0.31
62 3 0.04
66 26 0.37
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
Found at i:36440 original size:21 final size:22
Alignment explanation
Indices: 36414--36471 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
36404 GTGAATCGGG
*
36414 CTCTTGAACGGCGGACAG-GAC
1 CTCTTGAACGGAGGACAGAGAC
* *
36435 CTCTTGAAC-GATGACAGAGGC
1 CTCTTGAACGGAGGACAGAGAC
36456 CTCTTGAACGGTAGGA
1 CTCTTGAACGG-AGGA
36472 GGGGCTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 20 0.67
22 1 0.03
23 3 0.10
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (22 bp):
CTCTTGAACGGAGGACAGAGAC
Found at i:38579 original size:20 final size:20
Alignment explanation
Indices: 38556--38606 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38546 AGAAGTTTCT
*
38556 GAAACTTAAATTCACAACGC
1 GAAACTAAAATTCACAACGC
* * *
38576 GAAAATAAAAATCGCAACGC
1 GAAACTAAAATTCACAACGC
38596 GAAACTAAAAT
1 GAAACTAAAAT
38607 CGCGTTGCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.16
Consensus pattern (20 bp):
GAAACTAAAATTCACAACGC
Found at i:39136 original size:20 final size:20
Alignment explanation
Indices: 39108--39227 Score: 131
Period size: 20 Copynumber: 6.0 Consensus size: 20
39098 GCGTAAAAAT
*
39108 ATTTAACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
39128 ATTTGACTATCGCATTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
39148 ATTTGACT-TTGTGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
39167 ATTTAACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
39187 ATTTGACT-TCTGTGTTGCG-
1 ATTTGACTATC-GCGTTGCGA
39206 ATTT-ACATATTCGCGTTGCGA
1 ATTTGAC-TA-TCGCGTTGCGA
39227 A
1 A
39228 ATTGGAAACT
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.02
19 22 0.27
20 56 0.67
21 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:39176 original size:39 final size:39
Alignment explanation
Indices: 39121--39227 Score: 155
Period size: 39 Copynumber: 2.7 Consensus size: 39
39111 TAACTATCGC
*
39121 GTTGCGAATTTGACTATCGCATTGCGAATTTGACTT-TGT
1 GTTGCGAATTT-ACTATCGCGTTGCGAATTTGACTTCTGT
39160 GTTGCGAATTTAACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTT-ACTATCGCGTTGCGAATTTGACTTCTGT
39200 GTTGCG-ATTTACATATTCGCGTTGCGAA
1 GTTGCGAATTTAC-TA-TCGCGTTGCGAA
39228 ATTGGAAACT
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
38 2 0.03
39 40 0.63
40 21 0.33
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (39 bp):
GTTGCGAATTTACTATCGCGTTGCGAATTTGACTTCTGT
Found at i:39263 original size:20 final size:19
Alignment explanation
Indices: 39214--39267 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
39204 CGATTTACAT
39214 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
39233 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
39253 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
39268 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:41502 original size:195 final size:193
Alignment explanation
Indices: 41178--41638 Score: 527
Period size: 195 Copynumber: 2.4 Consensus size: 193
41168 CGGAAAGAAA
* * * * * ** * * **
41178 ATTGTCACATTTTTAGTAACATAGTATATCGTCACCTAATAGTAGCATGGACGAC-ATTTATATA
1 ATTGTCACATTTTTAGTGACATAATATATCATTACCTAATAATATTATGAATGACGA-TTATGCA
* * * ** * * **
41242 TAACATCACTATATAATTAATATTCA-ATGACAACTAATTATGTCACTAAATTATGTAAAATTTC
65 TAACATCACTTTATAATTTATATT-ATATTACAGTTGATTACGTCACTAAATTAAATAAAATTTC
*** *
41306 GTTATTGAT-GATTTATATCGTCATGGATAATACATTAAAATCAACCTATATGTGACGAAAGAGA
129 GTTATTGATAG-TTTATATCGTCACAAATAATACATTAAAATCAACCTATATGTGACGAAAAAGA
41370 T
193 T
* *
41371 ATTGTCA-ATTTTTTTAGTGACATAATATAAAT-GTTACCTAATAATATTATGAATGACGTTTAT
1 ATTGTCACA--TTTTTAGTGACATAATAT--ATCATTACCTAATAATATTATGAATGACGATTAT
* *
41434 GCATAACGTCACTTTATAATTTATATTATATTACAGTTGATTACGTCACTAAATTAAATAAGATT
62 GCATAACATCACTTTATAATTTATATTATATTACAGTTGATTACGTCACTAAATTAAATAAAATT
* * * *
41499 TCGTTATTGATAGTTTATATTGTCACAAATAATGCATTAAAATCAACTTATATGTGATGAAAAAG
127 TCGTTATTGATAGTTTATATCGTCACAAATAATACATTAAAATCAACCTATATGTGACGAAAAAG
41564 AT
192 AT
*
41566 ATTGTCACATTTTTAGTGACATAATATATCATTACCTAATAATATTATGAATGATGATTATGCAT
1 ATTGTCACATTTTTAGTGACATAATATATCATTACCTAATAATATTATGAATGACGATTATGCAT
41631 AACATCAC
66 AACATCAC
41639 CATATATAAT
Statistics
Matches: 225, Mismatches: 34, Indels: 18
0.81 0.12 0.06
Matches are distributed among these distances:
192 3 0.01
193 46 0.20
194 35 0.16
195 137 0.61
196 4 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (193 bp):
ATTGTCACATTTTTAGTGACATAATATATCATTACCTAATAATATTATGAATGACGATTATGCAT
AACATCACTTTATAATTTATATTATATTACAGTTGATTACGTCACTAAATTAAATAAAATTTCGT
TATTGATAGTTTATATCGTCACAAATAATACATTAAAATCAACCTATATGTGACGAAAAAGAT
Found at i:42683 original size:19 final size:18
Alignment explanation
Indices: 42636--42685 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
42626 TATAATTAGA
*
42636 TAAATTAAATACATAAATAT
1 TAAA-TAAATA-AGAAATAT
*
42656 TAAAAAAATAAGAAATAT
1 TAAATAAATAAGAAATAT
42674 TAAACTAAATAA
1 TAAA-TAAATAA
42686 ACTCACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 11 0.42
19 11 0.42
20 4 0.15
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAATAAATAAGAAATAT
Found at i:45382 original size:54 final size:54
Alignment explanation
Indices: 45286--45403 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 54
45276 GGTTTTTGCG
* * * * * * ** *
45286 TAAGGCGTGGGCACGACTTCTTCATCCTAAGCTATCGCAGAAGAAGTCTGTAGT
1 TAAGGTGTGGACACAACTTATTCATCCTAAGATATCACAGAAGAAGTCTACAAT
* * *
45340 TAAGGTGTGGACACAACTTATTTATCCTGAGATATCACAGAAGTAGTCTACAAT
1 TAAGGTGTGGACACAACTTATTCATCCTAAGATATCACAGAAGAAGTCTACAAT
45394 TAAGGTGTGG
1 TAAGGTGTGG
45404 GTACGCCTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (54 bp):
TAAGGTGTGGACACAACTTATTCATCCTAAGATATCACAGAAGAAGTCTACAAT
Found at i:45667 original size:16 final size:16
Alignment explanation
Indices: 45631--45661 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
45621 GGAGACATTA
45631 AGTTTTATAATTTAAG
1 AGTTTTATAATTTAAG
45647 AGTTTTATAATTTAA
1 AGTTTTATAATTTAA
45662 TTGTTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
AGTTTTATAATTTAAG
Found at i:47403 original size:17 final size:17
Alignment explanation
Indices: 47371--47404 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47361 TTGACTTTGA
*
47371 CCAAAAAGTTAAATTTT
1 CCAAAAAGTCAAATTTT
*
47388 CCAAAAAGTCATATTTT
1 CCAAAAAGTCAAATTTT
47405 ATGTTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (17 bp):
CCAAAAAGTCAAATTTT
Found at i:52230 original size:32 final size:32
Alignment explanation
Indices: 52116--52358 Score: 169
Period size: 32 Copynumber: 7.6 Consensus size: 32
52106 ATTGATATTT
* * * **
52116 ATTATCTGAATGCGACAATGACACTACTATAA
1 ATTATCTGAATGCAACACTGACACTATTATGC
* * *
52148 ATTATCTAAATTGC-ACAAT-ACCACTATTGTGC
1 ATTATCTGAA-TGCAACACTGA-CACTATTATGC
* *
52180 ATTATCTGAATGCGACACTAACACTATTATGC
1 ATTATCTGAATGCAACACTGACACTATTATGC
*
52212 ATTATCTGAATGCAACACTG--A-TATTGATGTTA
1 ATTATCTGAATGCAACACTGACACTATT-ATG--C
* * * *
52244 ATTATTTGAATGGAACACTGACACTAATGTGC
1 ATTATCTGAATGCAACACTGACACTATTATGC
*
52276 ATTATCTGAATGCAACATTGACACTGATGTA--C
1 ATTATCTGAATGCAACACTGACACT-AT-TATGC
* *
52308 TTTATCTGAATGCAACA-TGGACACTATTGTGC
1 ATTATCTGAATGCAACACT-GACACTATTATGC
* * *
52340 TTTATATGAATACAACACT
1 ATTATCTGAATGCAACACT
52359 CTGCCAGTAT
Statistics
Matches: 170, Mismatches: 25, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
29 4 0.02
30 5 0.03
31 7 0.04
32 141 0.83
33 6 0.04
34 4 0.02
35 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (32 bp):
ATTATCTGAATGCAACACTGACACTATTATGC
Found at i:52248 original size:64 final size:64
Alignment explanation
Indices: 52116--52358 Score: 210
Period size: 64 Copynumber: 3.8 Consensus size: 64
52106 ATTGATATTT
* * * ** * *
52116 ATTATCTGAATGCGACAATGACACTACTATAAATTATCTAAATTGC-ACAAT-ACCACT-ATTGT
1 ATTATCTGAATGCGACACTGACACTATTGTGCATTATCTGAA-TGCAACACTGA-CACTGA-TGT
*
52178 GC
63 AC
* * * *
52180 ATTATCTGAATGCGACACTAACACTATTATGCATTATCTGAATGCAACACTGATATTGATGTTA-
1 ATTATCTGAATGCGACACTGACACTATTGTGCATTATCTGAATGCAACACTGACACTGATG-TAC
* * *
52244 ATTATTTGAATG-GAACACTGACACTAATGTGCATTATCTGAATGCAACATTGACACTGATGTAC
1 ATTATCTGAATGCG-ACACTGACACTATTGTGCATTATCTGAATGCAACACTGACACTGATGTAC
* * * * *
52308 TTTATCTGAATGCAACA-TGGACACTATTGTGCTTTATATGAATACAACACT
1 ATTATCTGAATGCGACACT-GACACTATTGTGCATTATCTGAATGCAACACT
52359 CTGCCAGTAT
Statistics
Matches: 146, Mismatches: 25, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
63 7 0.05
64 136 0.93
65 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (64 bp):
ATTATCTGAATGCGACACTGACACTATTGTGCATTATCTGAATGCAACACTGACACTGATGTAC
Found at i:54062 original size:14 final size:14
Alignment explanation
Indices: 54043--54071 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54033 AAGTTAATCA
54043 TGAAATTCAAAAGG
1 TGAAATTCAAAAGG
54057 TGAAATTCAAAAGG
1 TGAAATTCAAAAGG
54071 T
1 T
54072 CTACATACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (14 bp):
TGAAATTCAAAAGG
Found at i:56376 original size:935 final size:946
Alignment explanation
Indices: 54183--57943 Score: 5598
Period size: 947 Copynumber: 4.0 Consensus size: 946
54173 TGCTAGACCA
*
54183 TTTAGACTGCAG-T-TATTTAGGATGTTCAATGGTGTTTCTTAATCTACACAG-TAGAATAGTGG
1 TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCTACACAGATAGAATAGTGG
* * *
54245 AATAAAT-AATTTAAATTAGGTCATTTGCTTGGAAATTAAAACTCTAAAGCTGGAATTTTCTAGC
66 AATAGATAAATTTAAATTAGGTCATTTGCTTGGAAATT-AAACTCTAAAGATGAAATTTTCTAGC
* * * * * *
54309 CTTCTAC--TACATAGACTATAACAAGTTCGTG-TGATAAGCTTAAGAAATATTGAAATCAAATG
130 CTTCAACGACACATAGACTATAACAGGTTCTTGTTGATAAGCTTAAGAAATATTGAAATCGAATA
*
54371 ATCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGATGAAA
195 ATCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAA
* * *
54436 GTAGTAAGCTGATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTCTT
260 GTAGTAAGCTAATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTATG
54501 AATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTA
325 AATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTA
54566 ---T-T--A-TAA-GGGCC-AAGAGGTAATATTAAGAGCCCTGACTTTATGAAC-GGATTACATT
390 TTCTCTAAAGTAATGGGCCAAAGAGGTAATATTAAGAGCCCTGACTTTATGAACGGGATTACATT
* * * * * *
54621 CAAATCATGACATTGATAACTGTGTTGAGATGGA-TTTCTAACATAAACAAAGCAAATAT-AAAA
455 CAGATCATGACACTGATAACTGTGTCGAGATGAATTTTCTAACAAAAACAAAGCAAATATGAGAA
* *
54684 CACCAAGGTTAATAAATAAA-TAATAAAG-GCGGTAAGGCCTAAAGTTTGAATTGAGAATGAGTT
520 CACCAAGGTGAA-ATATAAATTAATAAAGTGC-GTAAGGCCTAAAGTTTGAATTGAGAATGAGTT
* * *
54747 TCGATGGAAGATAAACTAAAGGAGTAAAGAAACATCTGTTATAGTCAACTAGATACAAACACTGA
583 TCGATGGAAGATAAACTAAGGGAGTAAAGAAACATCTGTTATAGTCGACTAGATACAAACACTCA
* * * * *
54812 GAAATTATGTTTCTAGATTGATATTTCAACATTGCTTCTAATAATGGAGTCTACGAAACCTAAAA
648 GAAATTATGTTTCTAGATCGATATTTCAGCATTGCCTCTACTAAAGGAGTCTACGAAACCTAAAA
* * *
54877 AAGTGGAAGATTTTATAGAACTAAAATATGAACACTCCCTAAAAGGTCTATCACTACAGTACCAA
713 AAGTGGAAGATTTTAGAGAACTAAAATATGAACACTCTCTAAAAGGTCTAGCACTACAGTACCAA
* * * * *
54942 ACGTGCTCCCAAGAGCATTTTACACAATCACTAGCACTTTTTACTAACTTGTCAAAGGTCCAGCG
778 ATGTGCTCCCAAGAGCATTTTAAACAATCACTAGCACTTTTTGCTAACATGTCAAAGGTCCAACG
*
55007 GCTTCTCAAATGTATACATGAATGTATAGATA-CGATGTACATGATCACCAAACCAAAGAATCCC
843 GCTTCTCAAAGGTATACATGAATGTATAGA-AGCGATGTACATGATCACCAAACCAAAGAATCCC
* * * *
55071 TCAAAAAAAAACAAACCACTCTAAACGCTTTCCAAATTAACT
907 TC--AAAAAAAGAAACCACTCTAAACACCTTCCAAATTAACC
55113 TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCTACACAGATAGAATAGTGG
1 TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCTACACAGATAGAATAGTGG
*
55178 AATAGATAAATTTAAATTAGGTCATTTTCTTGGAAATTAAACTCTAAAGATGAAATTTTCTAGCC
66 AATAGATAAATTTAAATTAGGTCATTTGCTTGGAAATTAAACTCTAAAGATGAAATTTTCTAGCC
* * *
55243 TTCAATGACACA-A-ACTA-AACCGGTTCTTGTTGATAAGCTTAAGAAATATTGAAATTGAATAA
131 TTCAACGACACATAGACTATAACAGGTTCTTGTTGATAAGCTTAAGAAATATTGAAATCGAATAA
55305 TCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAAG
196 TCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAAG
* * *
55370 TAGTAAGCTAATAATCTTAGGAGGTAAGTCTGAAGTAGTAATGGAGGCAAGTCCAAGCTTTATGA
261 TAGTAAGCTAATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTATGA
*
55435 ATGAGTTTCATTCATGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTAT
326 ATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTAT
* * * * *
55500 TTTCCTAAAGTAATGGGCCAAATAGGTAATATTAAGAGGCATGACTTTATGAACGAGATTACATT
391 TCT-CTAAAGTAATGGGCCAAAGAGGTAATATTAAGAGCCCTGACTTTATGAACGGGATTACATT
* *
55565 CAGATCATGACACTGATAACTTTGTGTCAAGATGAATTTTCTAACAAAAACAAAGAAAATATGAG
455 CAGATCATGACACTGATAAC--TGTGTCGAGATGAATTTTCTAACAAAAACAAAGCAAATATGAG
*
55630 AACACCAAGG-GAAATATAAATTAATAAAG-GCGTAAGGCCTAATGTTTGAATTGAGAATGAGTT
518 AACACCAAGGTGAAATATAAATTAATAAAGTGCGTAAGGCCTAAAGTTTGAATTGAGAATGAGTT
* * *
55693 TCGATGAAAGAT-AATTAAGGGAGTAAAG-AACATCTGTTATAGTCGACTAGATATAAACACTCA
583 TCGATGGAAGATAAACTAAGGGAGTAAAGAAACATCTGTTATAGTCGACTAGATACAAACACTCA
* * *
55756 TAAATTATGTTTCTAGATCGATATTTTAGCATTGCCTCTACTAAAGGAGTCTACGAAACCTAAAC
648 GAAATTATGTTTCTAGATCGATATTTCAGCATTGCCTCTACTAAAGGAGTCTACGAAACCTAAAA
* * *
55821 AAGTGGATGATTTTAGAGAACTAAAATATGAACACTCTCTAAAAGGTCTAGTACTACAGTACCGA
713 AAGTGGAAGATTTTAGAGAACTAAAATATGAACACTCTCTAAAAGGTCTAGCACTACAGTACCAA
55886 ATGTGCTCCCAAGAGCATTTTAAACAATCACTAGCAC-TTTTGCTAACATG-CAAAGGTCCAACG
778 ATGTGCTCCCAAGAGCATTTTAAACAATCACTAGCACTTTTTGCTAACATGTCAAAGGTCCAACG
* *
55949 ACTTCTCAAAGGTATACATGAATGTATA-AAGATGTATGTACATGATCACCAAACCAAAGAATCC
843 GCTTCTCAAAGGTATACATGAATGTATAGAAG-CG-ATGTACATGATCACCAAACCAAAGAATCC
56013 CTC-AAAAAAGAAACCACTCTAAACACCTTCCAAATTAACC
906 CTCAAAAAAAGAAACCACTCTAAACACCTTCCAAATTAACC
* *
56053 TTTAGACTGCAG-T-TA-TTAGGAAGTTCAATGGTGATTCTT-AT-TACATAGATAGAATAGTGG
1 TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCTACACAGATAGAATAGTGG
*
56113 AATAGATAAATTTAAATTAGGTAATTTGC-TGGAAATTAAACTCTAAAGATGAAA-TTTCTAGCC
66 AATAGATAAATTTAAATTAGGTCATTTGCTTGGAAATTAAACTCTAAAGATGAAATTTTCTAGCC
*
56176 TTCAACG-CACATAGACTATAACAGGTTCTTTTTGATAAGCTTAAGAAATATTGAAATCGAATAA
131 TTCAACGACACATAGACTATAACAGGTTCTTGTTGATAAGCTTAAGAAATATTGAAATCGAATAA
*
56240 TCAAGAATGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAAG
196 TCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAAG
* * * *
56305 TAGTAAGCTGATAATCTTCGAAGGTAAGTCTAAAGTAGTCATGGAGGTAAGTCAAAGCTTTATGA
261 TAGTAAGCTAATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTATGA
* *
56370 ATGAGTTTCATTCAAGTGGTAAAGTTGAAGACTTTCTAACAATTGAATCATCTGATTAGAGGTAT
326 ATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTAT
*
56435 TCTGCTAAAGTAATGGGCCAAAGAGGTAATATTAAGAGCCCTGACTTTATGAATGGGATTACATT
391 TCT-CTAAAGTAATGGGCCAAAGAGGTAATATTAAGAGCCCTGACTTTATGAACGGGATTACATT
* *
56500 CAGATCATGACACTGAT-A---TGTCGAGATTAATTTTCTAACAAAAACAAAGCAAATACGAGAA
455 CAGATCATGACACTGATAACTGTGTCGAGATGAATTTTCTAACAAAAACAAAGCAAATATGAGAA
** *
56561 CACCAAGGTTAATGAAATATAAATTAATAAAGTTTGTAATGCCTAAAG-TTGAATTGAGAATGAG
520 CACCAAGG----TGAAATATAAATTAATAAAGTGCGTAAGGCCTAAAGTTTGAATTGAGAATGAG
56625 TTTCGATGGAAGATAAACTAAGGGAGTAAAGAAACATCTGTTATAGTCGACTAGATACAAACACT
581 TTTCGATGGAAGATAAACTAAGGGAGTAAAGAAACATCTGTTATAGTCGACTAGATACAAACACT
* * *
56690 TAGAAATTATGTTTCTAGATCGATATTTCAGCATTGCCTCTATTAAAGGAGTCTAAGAAACCTAA
646 CAGAAATTATGTTTCTAGATCGATATTTCAGCATTGCCTCTACTAAAGGAGTCTACGAAACCTAA
* *
56755 AAAAGTGGAAGATTTTAGAGAACAAAAATATGAACACTCTCTTAAAAGGTCTAGCACTACGGTAC
711 AAAAGTGGAAGATTTTAGAGAACTAAAATATGAACACTCTC-TAAAAGGTCTAGCACTACAGTAC
* *
56820 CAAATGTGCTCCCAAGAGCATTTTAAGCAATCACTAGCACTTTTTGCTAACTTGTCAAAGGTCCA
775 CAAATGTGCTCCCAAGAGCATTTTAAACAATCACTAGCACTTTTTGCTAACATGTCAAAGGTCCA
* * * * *
56885 GCTGCTTCTCAAAGGTATACATGAATGTATAGAAGCGATGTACATAATCATCAAACCAAACAATC
840 ACGGCTTCTCAAAGGTATACATGAATGTATAGAAGCGATGTACATGATCACCAAACCAAAGAATC
*
56950 CCTCAAAAAAAGAAACCACTCTAAATACCTTCCAAATTAACC
905 CCTCAAAAAAAGAAACCACTCTAAACACCTTCCAAATTAACC
*
56992 TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCCACACAGATAGAATAGTGG
1 TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCTACACAGATAGAATAGTGG
** * * *
57057 AATTTATAAATTTAAATTAGGTCATTTGCTTGGAAATTAAATTATAAAGATGAAATTTTATAGCC
66 AATAGATAAATTTAAATTAGGTCATTTGCTTGGAAATTAAACTCTAAAGATGAAATTTTCTAGCC
* * * *
57122 TTTAACGACACACAGACTATAACATGTTCTTGTTGATAATCTTAAGAAATATTGAAATCGAATAA
131 TTCAACGACACATAGACTATAACAGGTTCTTGTTGATAAGCTTAAGAAATATTGAAATCGAATAA
* *
57187 TCAAGAAAGTAATGTGATATTAATCCATGATAGTTTTAATATTATTAGGGGCACTCCGTTGAAAG
196 TCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAAG
57252 TAGTAAGCTAATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTATGA
261 TAGTAAGCTAATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTATGA
*
57317 ATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTAC
326 ATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTAT
* *
57382 TCTACTAAAGTAATGGGCCAAAGAGGTAATATTAAGATCCCTGACTTTATGAATGGGATTACATT
391 TCT-CTAAAGTAATGGGCCAAAGAGGTAATATTAAGAGCCCTGACTTTATGAACGGGATTACATT
* * * * *
57447 TAGATTATGACAC---TAACTTTGTGTCGAGATTAATTTCCTAACAAAAGCAAAGCAAATATGAG
455 CAGATCATGACACTGATAAC--TGTGTCGAGATGAATTTTCTAACAAAAACAAAGCAAATATGAG
* *
57509 AACACTAAGGTTAATGAAATATAAATTAAGAAAAGTG-GTAAGGCCTAAAGTTTGAATTGAGAAT
518 AACACCAAGG----TGAAATATAAATTAA-TAAAGTGCGTAAGGCCTAAAGTTTGAATTGAGAAT
* * * * * *
57573 AAGTTTCGATGGAAGATAAAATAAGGGAGTTAAGAAACATCTGTTATAATCCACTAGATACAAGC
578 GAGTTTCGATGGAAGATAAACTAAGGGAGTAAAGAAACATCTGTTATAGTCGACTAGATACAAAC
* ** *
57638 ACTCAGAAATTATATTTCTAGATCGATATTT-ATGCATTGTATCTACTAAAGGAGTCTACAAAAC
643 ACTCAGAAATTATGTTTCTAGATCGATATTTCA-GCATTGCCTCTACTAAAGGAGTCTACGAAAC
* * *
57702 CTAAACAAGTGGAAGATTTCAGAGAACTAAAATATGAACACTCTCTAAAAGGTC-CGCACTACAG
707 CTAAAAAAGTGGAAGATTTTAGAGAACTAAAATATGAACACTCTCTAAAAGGTCTAGCACTACAG
* *
57766 TA-CGAATGTGCT-CCAAGAGCATTTTAAGCAATCACTAGCACTTTTTGCTAA-ATTGTCAAAGG
772 TACCAAATGTGCTCCCAAGAGCATTTTAAACAATCACTAGCACTTTTTGCTAACA-TGTCAAAGG
* * * * *
57828 TCCAATGGTTTCTCAAAGGTATACATGAATGCATAGAAGTGATGTACAGGATCACCAAAACCAAA
836 TCCAACGGCTTCTCAAAGGTATACATGAATGTATAGAAGCGATGTACATGATCACC-AAACCAAA
*
57893 GAATCCCTCAAAAAAAGAAACCACTCTAAACACCTTCCAAATTAACA
900 GAATCCCTCAAAAAAAGAAACCACTCTAAACACCTTCCAAATTAACC
57940 TTTA
1 TTTA
57944 CCATTAATAT
Statistics
Matches: 2576, Mismatches: 194, Indels: 104
0.90 0.07 0.04
Matches are distributed among these distances:
929 47 0.02
930 12 0.00
931 1 0.00
932 50 0.02
933 281 0.11
934 108 0.04
935 375 0.15
936 133 0.05
937 82 0.03
938 44 0.02
939 88 0.03
940 51 0.02
941 6 0.00
942 67 0.03
943 76 0.03
944 254 0.10
945 38 0.01
946 73 0.03
947 442 0.17
948 76 0.03
949 10 0.00
950 88 0.03
951 174 0.07
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (946 bp):
TTTAGACTGCAGTTCTATTTAGGATGTTCAATGGTGATTCTTAATCTACACAGATAGAATAGTGG
AATAGATAAATTTAAATTAGGTCATTTGCTTGGAAATTAAACTCTAAAGATGAAATTTTCTAGCC
TTCAACGACACATAGACTATAACAGGTTCTTGTTGATAAGCTTAAGAAATATTGAAATCGAATAA
TCAAGAAAGTAATGTGATATTAATGCATGATAGTTTTAATATTATTGGGGGCACTCCGTTGAAAG
TAGTAAGCTAATAATCTTCGGAGGTAAGTCTGAAGTAGTCATGGAGGTAAGTCCAAGCTTTATGA
ATGAGTTTCATTCAAGTGGTCAAGTTGAAGACTTTCTAACACTTGAATCATCTGATTAGAGGTAT
TCTCTAAAGTAATGGGCCAAAGAGGTAATATTAAGAGCCCTGACTTTATGAACGGGATTACATTC
AGATCATGACACTGATAACTGTGTCGAGATGAATTTTCTAACAAAAACAAAGCAAATATGAGAAC
ACCAAGGTGAAATATAAATTAATAAAGTGCGTAAGGCCTAAAGTTTGAATTGAGAATGAGTTTCG
ATGGAAGATAAACTAAGGGAGTAAAGAAACATCTGTTATAGTCGACTAGATACAAACACTCAGAA
ATTATGTTTCTAGATCGATATTTCAGCATTGCCTCTACTAAAGGAGTCTACGAAACCTAAAAAAG
TGGAAGATTTTAGAGAACTAAAATATGAACACTCTCTAAAAGGTCTAGCACTACAGTACCAAATG
TGCTCCCAAGAGCATTTTAAACAATCACTAGCACTTTTTGCTAACATGTCAAAGGTCCAACGGCT
TCTCAAAGGTATACATGAATGTATAGAAGCGATGTACATGATCACCAAACCAAAGAATCCCTCAA
AAAAAGAAACCACTCTAAACACCTTCCAAATTAACC
Found at i:58888 original size:36 final size:33
Alignment explanation
Indices: 58790--58900 Score: 120
Period size: 36 Copynumber: 3.2 Consensus size: 33
58780 AACAAAAATT
58790 ATCTCACTTGAGATATTTTTCAT-TGAAAATTTTC
1 ATCTCACTTGAGATATTTTTC-TCTGAAAA-TTTC
* *
58824 ATCTCA-TTCGAGACA-GTTTCTCTAGAAAAAAGTTTC
1 ATCTCACTT-GAGATATTTTTCTCT-G--AAAA-TTTC
58860 ATCTCACTTGAGATATTTTTCTCTGAAAATTTC
1 ATCTCACTTGAGATATTTTTCTCTGAAAATTTC
58893 ATCTCACT
1 ATCTCACT
58901 CAGGACAGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
32 1 0.02
33 19 0.29
34 16 0.25
36 20 0.31
37 9 0.14
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (33 bp):
ATCTCACTTGAGATATTTTTCTCTGAAAATTTC
Found at i:59260 original size:36 final size:37
Alignment explanation
Indices: 59220--59314 Score: 95
Period size: 38 Copynumber: 2.5 Consensus size: 37
59210 TATCTCTATT
59220 GAGATATTTTCTCTTAAAATAA-ATT-TCATCTCAGTC
1 GAGATATTTTCTCTTAAAATAACATTGT-ATCTCAGTC
* * * * *
59256 GAGATAGTTTATCTTAAAACAAACATTGTATCTCATTT
1 GAGATATTTTCTCTTAAAA-TAACATTGTATCTCAGTC
*
59294 GAGATCTTTTCTCTTGAAAAT
1 GAGATATTTTCTCTT-AAAAT
59315 TTTGTTTTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
36 17 0.37
37 2 0.04
38 22 0.48
39 5 0.11
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (37 bp):
GAGATATTTTCTCTTAAAATAACATTGTATCTCAGTC
Found at i:59298 original size:38 final size:35
Alignment explanation
Indices: 59203--59298 Score: 86
Period size: 36 Copynumber: 2.6 Consensus size: 35
59193 CTCTGAGAAT
* * *
59203 AAAACTTTATCTC-TATTGAGATATTTTCTCTTAAA
1 AAAAATTTATCTCAT-TTGAGATAGTTTATCTTAAA
* * *
59238 ATAAATTTCATCTCAGTCGAGATAGTTTATCTTAAA
1 AAAAATTT-ATCTCATTTGAGATAGTTTATCTTAAA
59274 ACAAACATTGTATCTCATTTGAGAT
1 A-AAA-ATT-TATCTCATTTGAGAT
59299 CTTTTCTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
35 6 0.13
36 23 0.49
37 2 0.04
38 15 0.32
39 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (35 bp):
AAAAATTTATCTCATTTGAGATAGTTTATCTTAAA
Found at i:59689 original size:34 final size:35
Alignment explanation
Indices: 59641--59721 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 35
59631 ACTTAAAGGA
*
59641 CATCCATAATTTGACTTAACCCGCAAA-GAGGAGT
1 CATCCATAACTTGACTTAACCCGCAAATGAGGAGT
* *
59675 CATCCATAACTTGACTTAACTCGCAAATGAGGATT
1 CATCCATAACTTGACTTAACCCGCAAATGAGGAGT
* *
59710 CAACCTTAACTT
1 CATCCATAACTT
59722 CAGTTTCCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 25 0.61
35 16 0.39
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (35 bp):
CATCCATAACTTGACTTAACCCGCAAATGAGGAGT
Done.