Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007870.1 Hibiscus syriacus cultivar Beakdansim tig00110245_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: 30188
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:7616 original size:29 final size:27
Alignment explanation
Indices: 7572--7640 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 27
7562 GTATTTCGCT
7572 TGAAAAAA-AAATGAAAAAGACAAAAAAA
1 TGAAAAAATAAA-GAAAAAGA-AAAAAAA
*
7600 TGAAAAAATGAAAGAAAGAGAAAAAAAA
1 TGAAAAAAT-AAAGAAAAAGAAAAAAAA
7628 TGAGAAAAATAAA
1 TGA-AAAAATAAA
7641 AGGAGGGTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 21 0.57
29 13 0.35
30 3 0.08
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.09
Consensus pattern (27 bp):
TGAAAAAATAAAGAAAAAGAAAAAAAA
Found at i:7642 original size:29 final size:30
Alignment explanation
Indices: 7573--7642 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
7563 TATTTCGCTT
7573 GAAAAA-AAAATGAAAAAGACAAAAAAATGA
1 GAAAAATAAAA-GAAAAAGACAAAAAAATGA
* *
7603 -AAAAATGAAAGAAAGAGA-AAAAAAATGA
1 GAAAAATAAAAGAAAAAGACAAAAAAATGA
7631 GAAAAATAAAAG
1 GAAAAATAAAAG
7643 GAGGGTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 10 0.29
29 22 0.63
30 3 0.09
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (30 bp):
GAAAAATAAAAGAAAAAGACAAAAAAATGA
Found at i:8823 original size:48 final size:48
Alignment explanation
Indices: 8765--9472 Score: 783
Period size: 48 Copynumber: 15.6 Consensus size: 48
8755 ATGGATCAAC
* * *
8765 TCTCCCAGATTTGATATTCCCTTCAGAGTAAGTGAAACAGGTCTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
8813 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * * * *
8856 T-GCC-ATATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
*
8902 TCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * * * *
8945 T-GCC-ATATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * *
8991 TCTCAAAGATTTGATATTCCCCTCAGAGTAAGTGGAACAAGTCTCTAT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * * * *
9039 TCTCCAAGATCTGATATTCCTTTTAGAGTAAGCGGAACAGGTCTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
9087 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * *
9130 T-GCC-AGATTTGATATTCCCTTCAGAGTAAGTGAAAC-A-TGTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
9174 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * * * *
9217 T-GCC-ATATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * *
9263 TCTCAAAGATTTGATATTCCCCTCAGAGTAAGTGGAACAAGTCTCTAT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* *
9311 TCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCT
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
9359 TCTCCAAGA-TTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* * *
9401 T-GCC-AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-T
1 TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
* *
9446 TTTCCATGATTTGATATTCCCTTCAGA
1 TCTCCAAGATTTGATATTCCCTTCAGA
9473 AGAAACGAAA
Statistics
Matches: 551, Mismatches: 71, Indels: 77
0.79 0.10 0.11
Matches are distributed among these distances:
40 4 0.01
41 155 0.28
42 8 0.01
43 8 0.01
44 9 0.02
45 10 0.02
46 36 0.07
47 52 0.09
48 269 0.49
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (48 bp):
TCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCT
Found at i:8927 original size:89 final size:89
Alignment explanation
Indices: 8769--9472 Score: 1047
Period size: 89 Copynumber: 7.8 Consensus size: 89
8759 ATCAACTCTC
* * *
8769 CCAGATTTGATATTCCCTTCAGAGTAAGTGAAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
8834 TTCAGAGTAAGTGGAACAAGTCTG
66 TTCAGAGTAAGTGGAACAAGTCTG
* *
8858 CCATATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
8923 TTCAGAGTAAGTGGAACAAGTCTG
66 TTCAGAGTAAGTGGAACAAGTCTG
* *
8947 CCATATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
9012 CTCAGAGTAAGTGGAACAAGTCTCTATTCT
66 TTCAGAGTAAGTGGAACAAG--TC---T-G
* *
9042 CCAAGATCTGATATTCCTTTTAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
9107 CTTCAGAGTAAGTGGAACAAGTCTG
65 CTTCAGAGTAAGTGGAACAAGTCTG
* * * *
9132 CCAGATTTGATATTCCCTTCAGAGTAAGTGAAACA--TGTCTCTTCTCCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
9195 TTCAGAGTAAGTGGAACAAGTCTG
66 TTCAGAGTAAGTGGAACAAGTCTG
* *
9219 CCATATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
9284 CTCAGAGTAAGTGGAACAAGTCTCTATTCT
66 TTCAGAGTAAGTGGAACAAG--TC---T-G
*
9314 CCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCCAAGA-TTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
9378 CTTCAGAGTAAGTGGAACAAGTCTG
65 CTTCAGAGTAAGTGGAACAAGTCTG
* * *
9403 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCATGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
9467 TTCAGA
66 TTCAGA
9473 AGAAACGAAA
Statistics
Matches: 562, Mismatches: 36, Indels: 35
0.89 0.06 0.06
Matches are distributed among these distances:
87 90 0.16
88 55 0.10
89 243 0.43
90 3 0.01
91 5 0.01
93 2 0.00
94 4 0.01
95 34 0.06
96 126 0.22
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (89 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAGTCTG
Found at i:9268 original size:272 final size:272
Alignment explanation
Indices: 8765--9472 Score: 1238
Period size: 272 Copynumber: 2.6 Consensus size: 272
8755 ATGGATCAAC
* * * *
8765 TCTCCCAGATTTGATATTCCCTTCAGAGTAAGTGAAACAGGTCTCTCTTCTCCAAGATTTGATAT
1 TCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATAT
* *
8830 TCCCTTCAGAGTAAGTGGAACAAGTCTGCCATATCTGATATTCCCTTCAGAGTAAGCGGAACAGG
66 TCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACA--
* *
8895 TCTCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCATATCTGATAT
129 TGTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCATATCTGATAT
8960 TCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCCTCAGAGTAAGTG
194 TCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCCTCAGAGTAAGTG
9025 GAACAAGTCTCTAT
259 GAACAAGTCTCTAT
* *
9039 TCTCCAAGATCTGATATTCCTTTTAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATAT
1 TCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATAT
* *
9104 TCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATTTGATATTCCCTTCAGAGTAAGTGAAACATG
66 TCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATG
9169 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCATATCTGATATTC
131 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCATATCTGATATTC
9234 CCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCCTCAGAGTAAGTGGA
196 CCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCCTCAGAGTAAGTGGA
9299 ACAAGTCTCTAT
261 ACAAGTCTCTAT
*
9311 TCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTCTCCAAGA-TTGATAT
1 TCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATAT
*
9375 TCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGG
66 TCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATG
* *
9440 TCTCTTTTTCCATGATTTGATATTCCCTTCAGA
131 TCTC-TTCTCCAAGATTTGATATTCCCTTCAGA
9473 AGAAACGAAA
Statistics
Matches: 413, Mismatches: 20, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
271 73 0.18
272 222 0.54
274 118 0.29
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (272 bp):
TCTCCAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATAT
TCCCTTCAGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATG
TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCATATCTGATATTC
CCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCCTCAGAGTAAGTGGA
ACAAGTCTCTAT
Found at i:19318 original size:5 final size:5
Alignment explanation
Indices: 19305--19603 Score: 139
Period size: 5 Copynumber: 58.6 Consensus size: 5
19295 AATATTATTA
*
19305 ATAAT ATAAC ATAAT ATAAT ATAAT ATAAT A-AAT AT-AT AATAAT A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
* * *
19353 AATACT ATAA- ATAAT AT-AT AATATAT GTACTAT ATAA- AT-AT ATACT
1 -ATAAT ATAAT ATAAT ATAAT -ATA-AT ATA--AT ATAAT ATAAT ATAAT
* *
19399 ATACT ATAAT ATAAT ATAAT ACATAAT ATACTAT ATAA- AT-AT ATACT
1 ATAAT ATAAT ATAAT ATAAT --ATAAT ATA--AT ATAAT ATAAT ATAAT
19446 ATAAT ATAA- ATAACAT ATAAT AT-AT ATAAT ATAAT ATAGTACT ATAAT
1 ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATA--A-T ATAAT
* * *
19494 AT-AT AATAAT ATACTGT ATAAT -T-AT ATACT AT-AT A-AAT ATTAT
1 ATAAT -ATAAT ATA--AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
19537 ATGATAT ATAAT ATGA- ATAAT ATAAAT GTTAT ATAAT AT-AT ACTATAT
1 AT-A-AT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT A-TA-AT
*
19585 AATAAT ATAAC ATAAT ATA
1 -ATAAT ATAAT ATAAT ATA
19604 TAATACTATA
Statistics
Matches: 229, Mismatches: 24, Indels: 82
0.68 0.07 0.24
Matches are distributed among these distances:
3 4 0.02
4 44 0.19
5 126 0.55
6 18 0.08
7 32 0.14
8 5 0.02
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:19369 original size:58 final size:57
Alignment explanation
Indices: 19294--19606 Score: 157
Period size: 62 Copynumber: 5.2 Consensus size: 57
19284 AACCAAAAGT
* *
19294 TAATATTATTAATAATATAACATAATATAATATAATATAATA-AATATATAATAATAAA
1 TAATACTATAAATAATATAA-ATAATATAATATAATATAATACAATATATAAT-ATAAA
* *
19352 TAATACTATAAATAATATATAATATATGTACTATATAA-ATATATACTATACTATAATATAATA
1 TAATACTATAAATAATATA-AATA-ATATA--ATATAATATA-ATACAATA-TATAATATAA-A
*
19415 TAATAC-ATAATATACTATATAAAT-ATATACTATAATATAAATA-ACATATAATATATATAATA
1 TAATACTATAA-ATA--ATATAAATAATATAATATAATAT-AATACA-ATAT-ATA-ATATAA-A
* * *
19477 TAATA-TAGTACTATAATATATAATAATATACTGTATAAT-TATATACTATATA-AATATTATAT
1 TAATACTA-TA-AATAATATA-AATAATATA--ATATAATATA-ATACAATATATAATA-TA-A-
19539 GA
57 -A
* * * *
19541 TATATAATATGAATAATATAAAT-GT-T-ATATAATAT-ATACTATATAATAATATAACA
1 TA-ATACTATAAATAATATAAATAATATAATATAATATAATACAATAT-ATAATATAA-A
19597 TAATA-TATAA
1 TAATACTATAA
19607 TACTATATAC
Statistics
Matches: 205, Mismatches: 17, Indels: 70
0.70 0.06 0.24
Matches are distributed among these distances:
54 4 0.02
55 3 0.01
56 3 0.01
57 10 0.05
58 29 0.14
59 10 0.05
60 9 0.04
61 29 0.14
62 37 0.18
63 32 0.16
64 22 0.11
65 15 0.07
66 2 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (57 bp):
TAATACTATAAATAATATAAATAATATAATATAATATAATACAATATATAATATAAA
Found at i:19376 original size:7 final size:7
Alignment explanation
Indices: 19323--19673 Score: 154
Period size: 7 Copynumber: 47.4 Consensus size: 7
19313 ACATAATATA
19323 ATATAAT
1 ATATAAT
19330 ATAATAAAT
1 AT-AT-AAT
19339 ATATAAT
1 ATATAAT
19346 A-ATAA-
1 ATATAAT
19351 ATAATACTAT
1 AT-ATA--AT
*
19361 AAATAAT
1 ATATAAT
19368 ATATAAT
1 ATATAAT
*
19375 ATATGTACT
1 ATA--TAAT
19384 ATATAAAT
1 ATAT-AAT
*
19392 ATATACT
1 ATATAAT
19399 ATACT-AT
1 ATA-TAAT
19406 AATATAAT
1 -ATATAAT
19414 ATAATACAT
1 AT-ATA-AT
*
19423 AATATACT
1 -ATATAAT
19431 ATATAA-
1 ATATAAT
19437 ATAT-AT
1 ATATAAT
19443 ACTATAAT
1 A-TATAAT
*
19451 ATAAATAAC
1 AT--ATAAT
19460 ATATAAT
1 ATATAAT
19467 ATAT-AT
1 ATATAAT
19473 AATATAAT
1 -ATATAAT
19481 ATAGT-A-
1 ATA-TAAT
*
19487 CTATAAT
1 ATATAAT
19494 ATATAAT
1 ATATAAT
*
19501 AATATACT
1 -ATATAAT
*
19509 GTATAATT
1 ATATAA-T
*
19517 ATATACT
1 ATATAAT
19524 ATATAA-
1 ATATAAT
19530 ATAT--T
1 ATATAAT
*
19535 ATATGAT
1 ATATAAT
19542 ATATAAT
1 ATATAAT
19549 ATGAATAAT
1 AT--ATAAT
19558 ATA-AATGTT
1 ATATAA---T
19567 ATATAAT
1 ATATAAT
*
19574 ATATACT
1 ATATAAT
19581 ATATAAT
1 ATATAAT
19588 A-AT-AT
1 ATATAAT
*
19593 AACATAAT
1 -ATATAAT
19601 ATATAAT
1 ATATAAT
19608 ACTATATACT
1 A-TATA-A-T
*
19618 ATATACT
1 ATATAAT
*
19625 ATTACAAT
1 A-TATAAT
*
19633 ATATATGTT
1 ATATA--AT
19642 ATATAAT
1 ATATAAT
* *
19649 ACCATACT
1 A-TATAAT
19657 ATATAAT
1 ATATAAT
19664 ATATAAT
1 ATATAAT
19671 ATA
1 ATA
19674 GTATAACAAT
Statistics
Matches: 265, Mismatches: 32, Indels: 94
0.68 0.08 0.24
Matches are distributed among these distances:
5 9 0.03
6 23 0.09
7 125 0.47
8 53 0.20
9 48 0.18
10 7 0.03
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:19498 original size:87 final size:83
Alignment explanation
Indices: 19323--19673 Score: 236
Period size: 93 Copynumber: 4.1 Consensus size: 83
19313 ACATAATATA
* *
19323 ATATAATATAATAAAT-ATATAATAATAAATA-ATACTATAA-AT-AAT-ATATAATATATGTAC
1 ATATAATATAATACATAATATACTAATAAATATATACTATAATATAAATAATATAATATATGTA-
19383 TATATAAATATATACTATACTAT
65 -ATAT-AATATATACTATA--AT
19406 AATATAATATAATACATAATATACTATATAAATATATACTATAATATAAATAACATATAATATAT
1 -ATATAATATAATACATAATATACTA-ATAAATATATACTATAATATAAAT-A-ATATAATATAT
*
19471 ATAATATAATATAGTACTATAAT
62 GTAATATAATATA-TACTATAAT
19494 ATATAATA-ATATACTGTATAATTATATACTATATAAATAT-TA-TATGATATATAATATGAATA
1 ATATAATATA-ATAC---AT-A--ATATACTA-ATAAATATATACTAT-A-ATATAA-AT-AATA
* *
19556 -ATATAAATGTTATATAATATATACTAT-AT
54 TA-ATATATGTAATATAATATATACTATAAT
* *
19585 A-ATAATAT-A-ACATAATATA-TAAT-ACTATATACTAT-ATACT-ATTACA-AT-ATATATGT
1 ATATAATATAATACATAATATACTAATAAATATATACTATAATA-TAAATA-ATATAATATATGT
* *
19641 TATATAATACCATACTATATAAT
64 AATATAATA-TATAC--TATAAT
19664 ATATAATATA
1 ATATAATATA
19674 GTATAACAAT
Statistics
Matches: 224, Mismatches: 11, Indels: 67
0.74 0.04 0.22
Matches are distributed among these distances:
75 16 0.07
76 6 0.03
77 2 0.01
78 7 0.03
79 8 0.04
80 11 0.05
81 5 0.02
82 5 0.02
84 16 0.07
85 9 0.04
86 8 0.04
87 21 0.09
88 6 0.03
89 10 0.04
90 19 0.08
91 7 0.03
92 23 0.10
93 42 0.19
94 3 0.01
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (83 bp):
ATATAATATAATACATAATATACTAATAAATATATACTATAATATAAATAATATAATATATGTAA
TATAATATATACTATAAT
Found at i:19520 original size:25 final size:25
Alignment explanation
Indices: 19320--19668 Score: 136
Period size: 25 Copynumber: 13.9 Consensus size: 25
19310 ATAACATAAT
* *
19320 ATAATATAATATAATAAATATATAATA
1 ATAATATACTAT-ATAATTATAT-ATA
*
19347 ATAAATAATACTATA-AATAATATATA
1 AT-AAT-ATACTATATAATTATATATA
* *
19373 ATATATGTACTATATAAATATATACT-
1 ATA-ATATACTATATAATTATATA-TA
*
19399 ATACTATA--ATATAA-TATA-ATA
1 ATAATATACTATATAATTATATATA
19420 CATAATATACTATATAAATATATACTATA
1 -ATAATATACTATAT-AAT-TATA-TATA
*
19449 ATATAAATAAC-ATATAA-TATATATA
1 ATA-ATAT-ACTATATAATTATATATA
*
19474 AT-ATA-A-TATAGTACTATAATATATA
1 ATAATATACTATA-TA--ATTATATATA
*
19499 ATAATATACTGTATAATTATATACTA
1 ATAATATACTATATAATTATATA-TA
*
19525 TATAA-ATA-T-TAT-ATGATATATA
1 -ATAATATACTATATAATTATATATA
*
19547 AT-ATGAATAATATA-AATGT-TATATA
1 ATAAT--ATACTATATAAT-TATATATA
*
19572 AT-ATATACTATATAATAATATA-A
1 ATAATATACTATATAATTATATATA
*
19595 CATAATATA-TA-AT-ACTATATACTA
1 -ATAATATACTATATAATTATATA-TA
* *
19619 TATACTATTACAATATATATGT-TATATA
1 -ATAATA-TACTATATA-AT-TATATATA
**
19647 ATACCATACTATATAA-TATATA
1 ATAATATACTATATAATTATATA
19669 ATATAGTATA
Statistics
Matches: 250, Mismatches: 26, Indels: 95
0.67 0.07 0.26
Matches are distributed among these distances:
20 2 0.01
21 7 0.03
22 21 0.08
23 29 0.12
24 30 0.12
25 58 0.23
26 38 0.15
27 27 0.11
28 14 0.06
29 21 0.08
30 3 0.01
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAATATACTATATAATTATATATA
Found at i:19635 original size:107 final size:106
Alignment explanation
Indices: 19446--19645 Score: 246
Period size: 107 Copynumber: 1.9 Consensus size: 106
19436 AATATATACT
*
19446 ATAATATAAATAACATATAATATATATAATATAATATAGTACTATAATATATAATAATATACTGT
1 ATAATATAAATAACATATAATATATATAATATAATATAG-ACTATAATATATAATAATATACTAT
* *
19511 ATAATTATATACTATATAAATATTATATGATATATAATATGA
65 ATAACTATATACAATATAAATATTATATGATATATAATATGA
***
19553 ATAATATAAATGTTATATAATATATACTATATAATAATATA-AC-ATAATATATAATACTATATA
1 ATAATATAAATAACATATAATATATA-TA-AT-ATAATATAGACTATAATATATAATA--ATATA
* *
19616 CTATAT-ACTAT-TACAATATATATGTTATAT
61 CTATATAACTATATACAATATAAATATTATAT
19646 AATACCATAC
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
107 52 0.65
108 8 0.10
109 12 0.15
110 8 0.10
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (106 bp):
ATAATATAAATAACATATAATATATATAATATAATATAGACTATAATATATAATAATATACTATA
TAACTATATACAATATAAATATTATATGATATATAATATGA
Found at i:25229 original size:2 final size:2
Alignment explanation
Indices: 25222--25267 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
25212 AAAAGAGGGA
25222 AT AT AT 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 AT AT AT
25264 AT AT
1 AT AT
25268 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25272 original size:2 final size:2
Alignment explanation
Indices: 25267--25291 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25257 TATATATATA
25267 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
25292 ATATATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:25308 original size:14 final size:14
Alignment explanation
Indices: 25291--25319 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25281 TGTGTGTGTG
25291 TATATATATGTATA
1 TATATATATGTATA
25305 TATATATATGTATA
1 TATATATATGTATA
25319 T
1 T
25320 GAAAGAAGAA
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATATGTATA
Done.