Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007906.1 Hibiscus syriacus cultivar Beakdansim tig00110300_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: 551901
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:473050 original size:22 final size:23
Alignment explanation
Indices: 473003--473063 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
472993 TAATTATTAA
* *
473003 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
473024 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
473047 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
473064 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:473349 original size:18 final size:20
Alignment explanation
Indices: 473322--473359 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
473312 TAATAAAATT
473322 ATAAAAAAA-TA-TTTAATA
1 ATAAAAAAATTATTTTAATA
*
473340 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
473360 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:473545 original size:20 final size:20
Alignment explanation
Indices: 473508--473546 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
473498 TTTCCAGATG
**
473508 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
473528 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
473547 TAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:473556 original size:15 final size:15
Alignment explanation
Indices: 473520--473571 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
473510 TTCCAGAAAT
**
473520 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
473535 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
473549 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
473564 GTAATTCA
1 GTAATTCA
473572 TTTTTCGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:474616 original size:18 final size:18
Alignment explanation
Indices: 474581--474616 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
474571 GAAAATGGAA
* *
474581 CGCTATATTTGACTAGTT
1 CGCTATATTTAACCAGTT
474599 CGCTATATTTAACCAGTT
1 CGCTATATTTAACCAGTT
474617 AATGAAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (18 bp):
CGCTATATTTAACCAGTT
Found at i:483452 original size:18 final size:17
Alignment explanation
Indices: 483431--483491 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
483421 GAAGATATAT
*
483431 AGAAAAACACACACAAAA
1 AGAAAAACAAACA-AAAA
483449 AGAAAGTAA-AAACAAAAA
1 AGAAA--AACAAACAAAAA
483467 AGAAAAACAAA-AGAAAA
1 AGAAAAACAAACA-AAAA
483484 AGAGAAAA
1 AGA-AAAA
483492 AGAAAAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 3 0.08
17 10 0.27
18 18 0.49
19 4 0.11
20 2 0.05
ACGTcount: A:0.77, C:0.10, G:0.11, T:0.02
Consensus pattern (17 bp):
AGAAAAACAAACAAAAA
Found at i:483474 original size:13 final size:13
Alignment explanation
Indices: 483451--483506 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
483441 ACACAAAAAG
483451 AAAGTAAAAACAAA
1 AAAG-AAAAACAAA
483465 AAAGAAAAAC--A
1 AAAGAAAAACAAA
*
483476 AAAGAAAAAGAGAA
1 AAAGAAAAACA-AA
483490 AAAGAAAAGA-AAA
1 AAAGAAAA-ACAAA
483503 AAAG
1 AAAG
483507 GAGATAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 10 0.27
13 12 0.32
14 14 0.38
15 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAGAAAAACAAA
Found at i:483478 original size:19 final size:19
Alignment explanation
Indices: 483462--483506 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
483452 AAGTAAAAAC
483462 AAAAAAGAAAAACAAAAGA
1 AAAAAAGAAAAACAAAAGA
* *
483481 AAAAGAGAAAAAGAAAAGA
1 AAAAAAGAAAAACAAAAGA
483500 AAAAAAG
1 AAAAAAG
483507 GAGATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAACAAAAGA
Found at i:483500 original size:11 final size:11
Alignment explanation
Indices: 483464--483503 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
483454 GTAAAAACAA
*
483464 AAAAGAAAAAC
1 AAAAGAAAAAG
483475 AAAAGAAAAAG
1 AAAAGAAAAAG
483486 ---AGAAAAAG
1 AAAAGAAAAAG
483494 AAAAGAAAAA
1 AAAAGAAAAA
483504 AAGGAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
8 8 0.32
11 17 0.68
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:486519 original size:55 final size:55
Alignment explanation
Indices: 486444--486691 Score: 284
Period size: 55 Copynumber: 4.5 Consensus size: 55
486434 GTGTTTTTTT
* *
486444 AATTAAGTATGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
1 AATTAAGTCTAATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
* ** * *
486499 AATTAATTCTAATTTTCAGAAGTTTCTTGATGATTTTCAAATTAGTTTTTAAAGA
1 AATTAAGTCTAATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
* *
486554 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGA--TTTTAAAGA
1 AATTAAGTCTAATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
* * *** * * * *
486607 AATTAAGTCTGATTTTCATAAGTTTCTTGATGGTTTTTAAAAGAACTTTCAAAGA
1 AATTAAGTCTAATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
* * **
486662 AATTAAGCCTAATTTTTAGGGGTTTCTTGA
1 AATTAAGTCTAATTTTCAGAAGTTTCTTGA
486692 TGTTTTAAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
53 46 0.28
55 118 0.72
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (55 bp):
AATTAAGTCTAATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
Found at i:486661 original size:108 final size:108
Alignment explanation
Indices: 486447--486735 Score: 328
Period size: 108 Copynumber: 2.6 Consensus size: 108
486437 TTTTTTTAAT
* * *
486447 TAAGTATGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAATTAATTCTAAT
1 TAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGA--TTTTAAAGAAATTAAGTCTGAT
** ** *
486512 TTTCAGAAGTTTCTTGATGATTTTCAAATTAGTTTTTAAAGAAAC
64 TTTCAGAAGTTTCTTGATGATTTTCAAAAGAACTTTCAAAGAAAC
486557 TAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGATTTTAAAGAAATTAAGTCTGATTT
1 TAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGATTTTAAAGAAATTAAGTCTGATTT
* * * *
486622 TCATAAGTTTCTTGATGGTTTTTAAAAGAACTTTCAAAGAAAT
66 TCAGAAGTTTCTTGATGATTTTCAAAAGAACTTTCAAAGAAAC
* * * ** ** * * *
486665 TAAGCCTAATTTTTAGGGGTTTCTTGA-TGTTTTAAAATGAATTTGAAAAAAAAATTAAGTCTGA
1 TAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATG-ATTT--TAAAGAAATTAAGTCTGA
486729 TTTTCAG
63 TTTTCAG
486736 GGGTTTTTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
107 9 0.06
108 82 0.54
110 62 0.41
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (108 bp):
TAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGATTTTAAAGAAATTAAGTCTGATTT
TCAGAAGTTTCTTGATGATTTTCAAAAGAACTTTCAAAGAAAC
Found at i:486692 original size:55 final size:53
Alignment explanation
Indices: 486628--486797 Score: 162
Period size: 55 Copynumber: 3.1 Consensus size: 53
486618 ATTTTCATAA
*
486628 GTTTCTTGATGGTTTTTAAAAGAACTTTCAAAGAAATTAAGCCTAATTTTTAGGG
1 GTTTCTTGAT-GTTTTTAAAAGAA-TTTAAAAGAAATTAAGCCTAATTTTTAGGG
* * * *
486683 GTTTCTTGATG-TTTTAAAATGAATTTGAAAAAAAAATTAAGTCTGATTTTCAGGG
1 GTTTCTTGATGTTTTTAAAA-GAATTT--AAAAGAAATTAAGCCTAATTTTTAGGG
* * * * *
486738 GTTTTTTTTTGATGTTTTTAAATGAATTTTTAAAGAAACTAAGCTTAATTTTTAGGG
1 G---TTTCTTGATGTTTTTAAAAGAA-TTTAAAAGAAATTAAGCCTAATTTTTAGGG
486795 GTT
1 GTT
486798 CTTTGACAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
53 11 0.12
54 6 0.06
55 33 0.35
57 21 0.23
58 12 0.13
59 10 0.11
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (53 bp):
GTTTCTTGATGTTTTTAAAAGAATTTAAAAGAAATTAAGCCTAATTTTTAGGG
Found at i:486949 original size:41 final size:41
Alignment explanation
Indices: 486841--486953 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 41
486831 AGGATTTCTT
* * * *
486841 GATGAGTAAGTCCTTCAGGCCATCAATAAGTCTTTCTAGCAT
1 GATGA-TAAGTCCTTCAGGCTATCTATAAGTCTTTCAAGCAA
** *
486883 GAATCTTAAATCCTTCAGG-TCATCTATAAGTCTTTCAAGCAA
1 G-ATGATAAGTCCTTCAGGCT-ATCTATAAGTCTTTCAAGCAA
*
486925 GATGATAAGTCCTTCGGGCTATCTATAAG
1 GATGATAAGTCCTTCAGGCTATCTATAAG
486954 ACCTTCGGGT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 22 0.39
42 33 0.58
43 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (41 bp):
GATGATAAGTCCTTCAGGCTATCTATAAGTCTTTCAAGCAA
Found at i:487072 original size:59 final size:58
Alignment explanation
Indices: 486988--487197 Score: 192
Period size: 58 Copynumber: 3.6 Consensus size: 58
486978 TGAGTTTTTA
* * *
486988 GAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAGATTTTTTTTAAG
1 GAAACTAAGCCTAATTTTCAGGGGTTCCTTGATGATTATCTCCAAAGA-ATTTTTTAAG
* * ** *** *
487047 GAAACTAAGACTAATTTTTAGGGGTTCCTTGATGACAAAT-GAAAAAGAAAGGTTTTT-A-
1 GAAACTAAGCCTAATTTTCAGGGGTTCCTTGATGA-TTATCTCCAAAG-AA-TTTTTTAAG
* * * *
487105 GAAACTAAGCCTGATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGAATTTTTAAAG
1 GAAACTAAGCCTAATTTTCAGGGGTTCCTTGATGATTATCTCCAAAGAATTTTTTAAG
* * * *
487163 GAAGCTAAGCATAATTTTAAGGAGTTCCTTGATGA
1 GAAACTAAGCCTAATTTTCAGGGGTTCCTTGATGA
487198 CAACTGAAAA
Statistics
Matches: 115, Mismatches: 30, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
56 4 0.03
57 5 0.04
58 62 0.54
59 36 0.31
60 8 0.07
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (58 bp):
GAAACTAAGCCTAATTTTCAGGGGTTCCTTGATGATTATCTCCAAAGAATTTTTTAAG
Found at i:487129 original size:58 final size:57
Alignment explanation
Indices: 486981--487254 Score: 169
Period size: 58 Copynumber: 4.7 Consensus size: 57
486971 TTTCAAATGA
** *** **
486981 GTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAGATT
1 GTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATCGAAAAAGAAG
* * * * *
487038 TTTTTTAAGGAAACTAAGACTAATTTTTAGGGGTTCCTTGATGACAAAT-GAAAAAGAAAG
1 GTTTTT-A-GAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGA-AAATCGAAAAAG-AAG
* ** ***
487098 GTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGAA-
1 GTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATCGAAAAAGAAG
* * * * * * * *
487154 -TTTTTAAAGGAAGCTAAGCATAATTTTAAGGAGTTCCTTGATGACAA-CTGAAAATGAAAG
1 GTTTTT--A-GAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATC-GAAAAAG-AAG
* * * *
487214 ATTTGTAGAAACTAAGCTTGATTTTCAGGAGTTTCTTGATG
1 GTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
487255 TTTTTTAAAT
Statistics
Matches: 163, Mismatches: 42, Indels: 23
0.71 0.18 0.10
Matches are distributed among these distances:
55 5 0.03
57 11 0.07
58 96 0.59
59 39 0.24
60 8 0.05
61 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (57 bp):
GTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATCGAAAAAGAAG
Found at i:487228 original size:116 final size:117
Alignment explanation
Indices: 486986--487252 Score: 403
Period size: 116 Copynumber: 2.3 Consensus size: 117
486976 AATGAGTTTT
* * *
486986 TAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAGATTTTTTTTAAGGAAA
1 TAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGATATTTTTAAAGGAAA
* * * *
487051 CTAAGACTAATTTTTAGGGGTTCCTTGATGACAAATGAAAAAGAAAGGTTTT
66 CTAAGACTAATTTTAAGGAGTTCCTTGATGACAAATGAAAAAGAAAGATTTG
*
487103 TAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGA-ATTTTTAAAGGAAG
1 TAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGATATTTTTAAAGGAAA
* *
487167 CTAAG-CATAATTTTAAGGAGTTCCTTGATGACAACTGAAAATGAAAGATTTG
66 CTAAGAC-TAATTTTAAGGAGTTCCTTGATGACAAATGAAAAAGAAAGATTTG
* *
487219 TAGAAACTAAGCTTGATTTTCAGGAGTTTCTTGA
1 TAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGA
487253 TGTTTTTTAA
Statistics
Matches: 137, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
115 1 0.01
116 87 0.64
117 49 0.36
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (117 bp):
TAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGATATTTTTAAAGGAAA
CTAAGACTAATTTTAAGGAGTTCCTTGATGACAAATGAAAAAGAAAGATTTG
Found at i:487453 original size:18 final size:18
Alignment explanation
Indices: 487430--487467 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
487420 CCAGGAAAAG
487430 AATGAAGACTGCTCTAGC
1 AATGAAGACTGCTCTAGC
*
487448 AATGAAGACTGCTCTTGC
1 AATGAAGACTGCTCTAGC
487466 AA
1 AA
487468 CCATTTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (18 bp):
AATGAAGACTGCTCTAGC
Found at i:489316 original size:23 final size:23
Alignment explanation
Indices: 489272--489316 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
489262 TTCATTATAT
*
489272 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
489295 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
489317 AGTTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:495486 original size:64 final size:64
Alignment explanation
Indices: 495418--495574 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
495408 TTGAAGGTGT
* ***
495418 ATCGATGCATTAGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCAGTAATAATA-AAACATCGAATGCATATTA-T
495480 GC
63 GC
* * *
495482 ATCGATGCATAAGTCATGCATCGATGCATCCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
* * *
495546 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
495575 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
Found at i:496207 original size:23 final size:23
Alignment explanation
Indices: 496163--496207 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
496153 ATCATTATAT
*
496163 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
496186 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
496208 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:502376 original size:64 final size:64
Alignment explanation
Indices: 502308--502464 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
502298 TTGAAGGTGT
* ***
502308 ATCGATGCATTAGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCAGTAATAATA-AAACATCGAATGCATATTA-T
502370 GC
63 GC
* * *
502372 ATCGATGCATAAGTCATGCATCGATGCATCCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
* * *
502436 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
502465 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
Found at i:503973 original size:137 final size:138
Alignment explanation
Indices: 503692--504002 Score: 426
Period size: 137 Copynumber: 2.3 Consensus size: 138
503682 TCAAATGGAG
* * * * * ***
503692 AGTTCATAATGAGAAGAGCTTGTTCGACCTTAGCTTGATTTATCGCATATGGAGTTCAATCGGTA
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTCAATCAACA
* * * *
503757 ACACCTCACTTGAGGTATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGA
66 ACACCTCACTCGAGGGAT-AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAA
* *
503822 GGGAGAAGG
130 AGGAGAAGA
* *
503831 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCAACA
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTCAATCAACA
* * * *
503896 ACATCTCACTCGAGGGAT-ACATTTCCAGTGGAGAGTTCGTAATGAGAATAACTCATCCGATAAA
66 ACACCTCACTCGAGGGATAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAA
503960 GGAGAAGA
131 GGAGAAGA
503968 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
504003 TGTTTCCATC
Statistics
Matches: 152, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
137 82 0.54
139 70 0.46
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (138 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTCAATCAACA
ACACCTCACTCGAGGGATAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAA
GGAGAAGA
Found at i:511056 original size:32 final size:33
Alignment explanation
Indices: 511020--511092 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
511010 AACCTTTTTT
* *
511020 ATATTTTTAATTT-TGTAT-AAAAAATTATATAA
1 ATATTTTGAATTTAT-TATAAAAAAAATATATAA
* *
511052 ATATTATGAATTTAATTTTAAAAAAAATATATAA
1 ATATTTTGAATTT-ATTATAAAAAAAATATATAA
511086 ATATTTT
1 ATATTTT
511093 ACAATTTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
32 11 0.33
33 2 0.06
34 20 0.61
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (33 bp):
ATATTTTGAATTTATTATAAAAAAAATATATAA
Found at i:515428 original size:28 final size:28
Alignment explanation
Indices: 515396--515454 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
515386 GTATAGTCGT
515396 TGTTTCAAGCACTAACTCGACAATATAA
1 TGTTTCAAGCACTAACTCGACAATATAA
* ** *
515424 TGTTTCAAGCATTAGTTCGACGATATAA
1 TGTTTCAAGCACTAACTCGACAATATAA
515452 TGT
1 TGT
515455 AAATGAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (28 bp):
TGTTTCAAGCACTAACTCGACAATATAA
Found at i:516674 original size:25 final size:24
Alignment explanation
Indices: 516628--516674 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
516618 AGTGTTAGAG
* * *
516628 AAAATAAATTATTTGAAGGGATCC
1 AAAATAAATCATTTAAAAGGATCC
516652 AAAATGAAATCATTTAAAAGGAT
1 AAAAT-AAATCATTTAAAAGGAT
516675 TAGCGAAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATAAATCATTTAAAAGGATCC
Found at i:517798 original size:29 final size:32
Alignment explanation
Indices: 517748--517818 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 32
517738 ATTTAACTTG
517748 ATTTATTTAGAAGAAGATAAA-TTTAT-AA-T
1 ATTTATTTAGAAGAAGATAAATTTTATAAATT
*
517777 ATTTATTTAG-AGAATATAAAATTTTATGAAATT
1 ATTTATTTAGAAGAAGAT-AAATTTTAT-AAATT
517810 ATTTATTTA
1 ATTTATTTA
517819 TCAAATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 6 0.17
29 13 0.36
30 5 0.14
32 2 0.06
33 10 0.28
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.46
Consensus pattern (32 bp):
ATTTATTTAGAAGAAGATAAATTTTATAAATT
Found at i:519357 original size:19 final size:18
Alignment explanation
Indices: 519329--519371 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 18
519319 TTTTTTCATT
519329 GAAAAACCGAACCGAACC
1 GAAAAACCGAACCGAACC
519347 GAAAAACCCGAACCGAACC
1 GAAAAA-CCGAACCGAACC
519366 GAAAAA
1 GAAAAA
519372 ACTGATTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.53, C:0.30, G:0.16, T:0.00
Consensus pattern (18 bp):
GAAAAACCGAACCGAACC
Found at i:522168 original size:20 final size:19
Alignment explanation
Indices: 522143--522213 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
522133 TTACAATGAC
522143 AAAATAAAAAAACAGAAAA
1 AAAATAAAAAAACAGAAAA
* *
522162 TAAAATAAAAAAATAAGGAAA
1 -AAAATAAAAAAA-CAGAAAA
* *
522183 AAAATACAAAAACATAAAGA
1 AAAATAAAAAAACAGAAA-A
522203 AAAA-AAAAAAA
1 AAAATAAAAAAA
522214 TAAAACAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 9 0.21
20 28 0.67
21 5 0.12
ACGTcount: A:0.82, C:0.04, G:0.06, T:0.08
Consensus pattern (19 bp):
AAAATAAAAAAACAGAAAA
Found at i:522173 original size:22 final size:20
Alignment explanation
Indices: 522143--522218 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
522133 TTACAATGAC
*
522143 AAAAT-AAAAAAACAGAAAA
1 AAAATAAAAAAAAAAGAAAA
* *
522162 TAAAATAAAAAAATAAGGAAA
1 -AAAATAAAAAAAAAAGAAAA
522183 AAAATACAAAAACATAAAGAAAA
1 AAAATA-AAAAA-A-AAAGAAAA
522206 AAAA-AAAATAAAA
1 AAAATAAAA-AAAA
522219 CAATAGTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 12 0.26
21 20 0.43
22 4 0.09
23 10 0.22
ACGTcount: A:0.82, C:0.04, G:0.05, T:0.09
Consensus pattern (20 bp):
AAAATAAAAAAAAAAGAAAA
Found at i:522729 original size:42 final size:41
Alignment explanation
Indices: 522649--522729 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
522639 TAAAAACAAT
* * *
522649 CAAATAAAAAAAGAAAAAATTAAAATGTATATATAATAATA
1 CAAATAAAAAAAGAAAAAATAAAAATATATACATAATAATA
* * *
522690 CAAATAATAAAAGGAATAAATAAAAATATTTACATAATAA
1 CAAATAA-AAAAAGAAAAAATAAAAATATATACATAATAA
522730 ATGAAGGACT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 7 0.21
42 26 0.79
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.25
Consensus pattern (41 bp):
CAAATAAAAAAAGAAAAAATAAAAATATATACATAATAATA
Found at i:524766 original size:23 final size:23
Alignment explanation
Indices: 524739--524807 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
524729 GTCACCACAG
*
524739 CTCATATAAATGCACCGA-AGTGC
1 CTCATAGAAATGCACC-ATAGTGC
*
524762 CTCATAGAATTGCACCATAGTGC
1 CTCATAGAAATGCACCATAGTGC
* * * *
524785 CGCGTAGAATTGCACCGTAGTGC
1 CTCATAGAAATGCACCATAGTGC
524808 TATATAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
CTCATAGAAATGCACCATAGTGC
Found at i:524996 original size:103 final size:103
Alignment explanation
Indices: 524825--525042 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
524815 TAATGTCCAT
524825 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCA
524890 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
524928 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCA
524993 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
525031 AAGGACCACATA
1 AAGGACCACATA
525043 AACCCTCGAC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:526259 original size:21 final size:21
Alignment explanation
Indices: 526219--526264 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
526209 TTTTTGTTCG
* * *
526219 CTTGAAGGGGTATCGGTTCCT
1 CTTGAAGGGGTACCGATTCCC
*
526240 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
526261 CTTG
1 CTTG
526265 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:530223 original size:23 final size:23
Alignment explanation
Indices: 530196--530265 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
530186 GTCACCACAG
* * *
530196 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAATTGCACCGTAGTGC
530219 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
* *
530242 CGCGTAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
530265 C
1 C
530266 ATATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCATAGAATTGCACCGTAGTGC
Found at i:530453 original size:103 final size:103
Alignment explanation
Indices: 530284--530499 Score: 423
Period size: 103 Copynumber: 2.1 Consensus size: 103
530274 ATGTCCATAT
530284 GGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGA
1 GGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGA
530349 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
*
530387 GGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGA
1 GGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGA
530452 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
530490 GGACCACATA
1 GGACCACATA
530500 AACCCTCGAC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
GGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
Found at i:531716 original size:21 final size:21
Alignment explanation
Indices: 531676--531721 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
531666 TTTTTGTTCG
* * *
531676 CTTGAAGGGGTATCGGTTCCT
1 CTTGAAGGGGTACCGATTCCC
*
531697 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
531718 CTTG
1 CTTG
531722 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:535682 original size:23 final size:23
Alignment explanation
Indices: 535655--535724 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
535645 ATCATCACAG
*
535655 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAAATGCACCGAAGTGC
* *
535678 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAAATGCACCGAAGTGC
* * *
535701 CGCGTAGAATTGCACC-ATAGTGC
1 CTCATAGAAATGCACCGA-AGTGC
535724 C
1 C
535725 ATATAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (23 bp):
CTCATAGAAATGCACCGAAGTGC
Found at i:535912 original size:103 final size:103
Alignment explanation
Indices: 535741--535958 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
535731 TAATGTCCAT
535741 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
535806 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
535844 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
535909 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
535947 AAGGACCACATA
1 AAGGACCACATA
535959 AACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:537173 original size:21 final size:21
Alignment explanation
Indices: 537133--537178 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
537123 TTTTTGTTCG
* * *
537133 CTTGAAGGGGTATCGGTTCCT
1 CTTGAAGGGGTACCGATTCCC
*
537154 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
537175 CTTG
1 CTTG
537179 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:546890 original size:14 final size:14
Alignment explanation
Indices: 546871--546900 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
546861 AATATCCTCC
*
546871 ATCGTGAAGTTGAA
1 ATCGTGAAGTTAAA
546885 ATCGTGAAGTTAAA
1 ATCGTGAAGTTAAA
546899 AT
1 AT
546901 TGGATCTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (14 bp):
ATCGTGAAGTTAAA
Found at i:548262 original size:1 final size:1
Alignment explanation
Indices: 548256--548289 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
548246 ACCCTAAACG
*
548256 TTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
548290 CTTCTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:548269 original size:7 final size:7
Alignment explanation
Indices: 548257--548299 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
548247 CCCTAAACGT
548257 TTTTTTC
1 TTTTTTC
548264 TTTTTT-
1 TTTTTTC
*
548270 TTTTTTT
1 TTTTTTC
*
548277 TTTTTTT
1 TTTTTTC
548284 TTTTTTC
1 TTTTTTC
*
548291 TTCTTTC
1 TTTTTTC
548298 TT
1 TT
548300 CGACTTAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Done.