Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006986.1 Hibiscus syriacus cultivar Beakdansim tig00018006_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: 55521
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7155 original size:31 final size:31
Alignment explanation
Indices: 7120--7180 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
7110 GTTTCAAACA
* **
7120 TAACAAATTGGTCACTAATGTTATCTATTTG
1 TAACAAATCGGTCACTAACATTATCTATTTG
7151 TAACAAATCGGTCACTAACATTATCTATTT
1 TAACAAATCGGTCACTAACATTATCTATTT
7181 AGAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (31 bp):
TAACAAATCGGTCACTAACATTATCTATTTG
Found at i:8576 original size:2 final size:2
Alignment explanation
Indices: 8571--8818 Score: 81
Period size: 2 Copynumber: 123.5 Consensus size: 2
8561 TATATGAACC
* * * * *
8571 AT AT AT AT GT AT AA ACT AT AT AGT TT AT AT AT AA AA AT AT AT -T
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * *
8614 AT AT AT AT A- ACT AT AT A- AA AA ACT AT AT AGT TT AT AT -T AT
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* * *
8654 AT -T AT -T AT AT ACT AT AT AT AA ACT AT AT AT AT -T AT GT AT AA
1 AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * *
8695 ACT AT AT AGT GT AT AT AT AA AGT GT AT AT AT -T AT AT AT AT AA
1 A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * *
8737 ACT AT GT AT AT AA ACT AT AT AGT TT AT AT TT AT AT -T AT -T AT
1 A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * *
8778 AT ACT AT AT AT AA AT -T AT AT AT AT -T AT GT AT AA AT -T AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8818 A
1 A
8819 GTTTATTAAC
Statistics
Matches: 180, Mismatches: 39, Indels: 54
0.66 0.14 0.20
Matches are distributed among these distances:
1 13 0.07
2 152 0.84
3 15 0.08
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:8605 original size:20 final size:19
Alignment explanation
Indices: 8544--8841 Score: 128
Period size: 20 Copynumber: 15.8 Consensus size: 19
8534 ATAATATATC
*
8544 TATATAAACTA-ATA-CTA
1 TATATAAACTATATATTTA
* *
8561 TATATGAACCATATA--TA
1 TATATAAACTATATATTTA
*
8578 TGTATAAACTATATAGTTTA
1 TATATAAACTATATA-TTTA
*
8598 TATATAAA-AATATA-TTA
1 TATATAAACTATATATTTA
8615 TATATATAAC--TATA--TA
1 TATATA-AACTATATATTTA
8631 -A-A-AAACTATATAGTTTA
1 TATATAAACTATATA-TTTA
* * *
8648 TAT-TATATTATTATATACTA
1 TATATAAACTA-TATAT-TTA
8668 TATATAAACTATATATATTA
1 TATATAAACTATATAT-TTA
* *
8688 TGTATAAACTATATAGTGTA
1 TATATAAACTATATA-TTTA
*
8708 TATATAAAGTGTATATATTATA
1 TATATAAA--CTATATATT-TA
* *
8730 TATATAAACTATGTATATA
1 TATATAAACTATATATTTA
* * * *
8749 AACTATATAGTTTATATTTA
1 TA-TATAAACTATATATTTA
* *
8769 TAT-T--ATTATATA-CTA
1 TATATAAACTATATATTTA
*
8784 TATATAAATTATATATATTA
1 TATATAAACTATATAT-TTA
* *
8804 TGTATAAATTATATAGTTTA
1 TATATAAACTATATA-TTTA
*
8824 TTAACATAAACTATATAT
1 -T-ATATAAACTATATAT
8842 AAACAATATA
Statistics
Matches: 215, Mismatches: 36, Indels: 56
0.70 0.12 0.18
Matches are distributed among these distances:
12 3 0.01
13 1 0.00
14 5 0.02
15 6 0.03
16 9 0.04
17 38 0.18
18 15 0.07
19 14 0.07
20 87 0.40
21 10 0.05
22 27 0.13
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (19 bp):
TATATAAACTATATATTTA
Found at i:8618 original size:19 final size:21
Alignment explanation
Indices: 8574--8623 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
8564 ATGAACCATA
* *
8574 TATATGTATAAACTATATAGT
1 TATATATATAAACAATATAGT
8595 T-TATATATAAA-AATATA-T
1 TATATATATAAACAATATAGT
8613 TATATATATAA
1 TATATATATAA
8624 CTATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 9 0.35
21 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATATATAAACAATATAGT
Found at i:8621 original size:11 final size:11
Alignment explanation
Indices: 8607--8910 Score: 73
Period size: 11 Copynumber: 27.5 Consensus size: 11
8597 ATATATAAAA
8607 ATATATTATAT
1 ATATATTATAT
8618 ATATA--ACTAT
1 ATATATTA-TAT
* **
8628 ATAAAAAACTAT
1 ATATATTA-TAT
8640 ATAGT-TTATAT
1 ATA-TATTATAT
8651 -TATATTAT-T
1 ATATATTATAT
*
8660 ATATACTATAT
1 ATATATTATAT
* *
8671 ATAAACTATAT
1 ATATATTATAT
8682 ATATTATGTATAAACT
1 ATA-TAT-TAT--A-T
8698 ATATAGTGTATAT
1 ATATA-T-TATAT
*
8711 ATAAAGTGTATAT
1 ATATA-T-TATAT
8724 AT-TA-TATAT
1 ATATATTATAT
* * *
8733 ATAAACTATGT
1 ATATATTATAT
*
8744 ATATA-AACTAT
1 ATATATTA-TAT
8755 ATAGT-TTATAT
1 ATA-TATTATAT
*
8766 TTATATTAT-T
1 ATATATTATAT
*
8776 ATATACTATAT
1 ATATATTATAT
*
8787 ATA-AAT-TAT
1 ATATATTATAT
*
8796 ATATATTATGT
1 ATATATTATAT
*
8807 ATAAATTATAT
1 ATATATTATAT
* *
8818 AGTTTATTA-AC
1 A-TATATTATAT
* *
8829 ATAAACTATAT
1 ATATATTATAT
* **
8840 ATAAACAATAT
1 ATATATTATAT
*
8851 AGTTTATTA-AT
1 A-TATATTATAT
*
8862 ATAAATTATAT
1 ATATATTATAT
8873 ATGA-ATTATAT
1 AT-ATATTATAT
* *
8884 TTA-AATATAT
1 ATATATTATAT
* *
8894 ACATCTTATAT
1 ATATATTATAT
*
8905 TTATAT
1 ATATAT
8911 CAACAACAAT
Statistics
Matches: 218, Mismatches: 47, Indels: 56
0.68 0.15 0.17
Matches are distributed among these distances:
9 16 0.07
10 52 0.24
11 97 0.44
12 22 0.10
13 18 0.08
14 1 0.00
15 3 0.01
16 9 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (11 bp):
ATATATTATAT
Found at i:8649 original size:50 final size:52
Alignment explanation
Indices: 8583--8798 Score: 163
Period size: 54 Copynumber: 4.0 Consensus size: 52
8573 ATATATGTAT
8583 AAACTATATAGTTTATA-TATAAAAATATAT--TATATATATAACTATATAAA
1 AAACTATATAGTTTATATTATAAAAATATATACTATATATA-AACTATATAAA
** *
8633 AAACTATATAGTTTATATTATATTATTATATACTATATATAAACTATATATATTATGTA
1 AAACTATATAGTTTATATTATAAAAATATATACTATATATAAAC--TATATA--A---A
* * * *
8692 TAAACTATATAGTGTATA-TATAAAGTGTATATATTA-TATATATAAACTATGTATAT
1 -AAACTATATAGTTTATATTATAAA---AATATA-TACTATATATAAACTATATA-AA
** * *
8748 AAACTATATAGTTTATATTTATATTATTATATACTATATATAAATTATATA
1 AAACTATATAGTTTATA-TTATAAAAATATATACTATATATAAACTATATA
8799 TATTATGTAT
Statistics
Matches: 131, Mismatches: 17, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
50 17 0.13
51 10 0.08
52 3 0.02
53 10 0.08
54 25 0.19
55 16 0.12
56 1 0.01
57 4 0.03
59 7 0.05
60 21 0.16
62 15 0.11
63 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (52 bp):
AAACTATATAGTTTATATTATAAAAATATATACTATATATAAACTATATAAA
Found at i:8731 original size:9 final size:9
Alignment explanation
Indices: 8719--8809 Score: 54
Period size: 9 Copynumber: 10.7 Consensus size: 9
8709 ATATAAAGTG
8719 TATATATTA
1 TATATATTA
8728 TATATA-TA
1 TATATATTA
8736 -A-ACTATGTA
1 TATA-TAT-TA
* *
8745 TATAAACTA
1 TATATATTA
*
8754 TATA-GTT-
1 TATATATTA
8761 TATAT-TTA
1 TATATATTA
8769 TAT-TATTA
1 TATATATTA
8777 TATACTA-TA
1 TATA-TATTA
*
8786 TATAAATTA
1 TATATATTA
8795 TATATATTA
1 TATATATTA
*
8804 TGTATA
1 TATATA
8810 AATTATATAG
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
6 1 0.02
7 10 0.16
8 13 0.20
9 35 0.55
10 4 0.06
11 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (9 bp):
TATATATTA
Found at i:8809 original size:13 final size:13
Alignment explanation
Indices: 8677--8809 Score: 55
Period size: 13 Copynumber: 10.3 Consensus size: 13
8667 ATATATAAAC
8677 TATATATATTATG
1 TATATATATTATG
*
8690 TATAAACTATATAGTG
1 TATATA-TAT-TA-TG
*
8706 TATATATA--AAG
1 TATATATATTATG
* *
8717 TGTATATATTATA
1 TATATATATTATG
* *
8730 TATATAAACTATG
1 TATATATATTATG
* *
8743 TATATAAACTA--
1 TATATATATTATG
* *
8754 TATAGTTTA-TATT
1 TATA-TATATTATG
*
8767 TATAT-TATTATA
1 TATATATATTATG
*
8779 TACTATATATAAAT-
1 TA-TATATAT-TATG
8793 TATATATATTATG
1 TATATATATTATG
8806 TATA
1 TATA
8810 AATTATATAG
Statistics
Matches: 92, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
11 16 0.17
12 11 0.12
13 44 0.48
14 8 0.09
15 6 0.07
16 7 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (13 bp):
TATATATATTATG
Found at i:8841 original size:116 final size:110
Alignment explanation
Indices: 8555--8824 Score: 393
Period size: 116 Copynumber: 2.4 Consensus size: 110
8545 ATATAAACTA
* * *
8555 ATACTATATATGAAC--CATATA-TATGTATAAACTATATAGTTTATATATAAAAATATATTATA
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATATATAAATATATATTATA
8617 TATATAACTATATAAAAAACTATATAGTTTATATTATATTATTAT
66 TATATAACTATATAAAAAACTATATAGTTTATATTATATTATTAT
*
8662 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAAGTGTATATATT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATATATAAA---TATATATT
* *
8727 ATATATATAAACTATGTATATAAACTATATAGTTTATATTTATATTATTAT
63 ATATATAT-AACTATATA-AAAAACTATATAGTTTATA-TTATATTATTAT
* *
8778 ATACTATATATAAATTATATATATTATGTATAAATTATATAGTTTAT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTAT
8825 TAACATAAAC
Statistics
Matches: 145, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
107 14 0.10
109 5 0.03
110 29 0.20
113 15 0.10
114 8 0.06
115 18 0.12
116 56 0.39
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (110 bp):
ATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATATATAAATATATATTATA
TATATAACTATATAAAAAACTATATAGTTTATATTATATTATTAT
Found at i:8904 original size:116 final size:116
Alignment explanation
Indices: 8555--8904 Score: 307
Period size: 116 Copynumber: 3.1 Consensus size: 116
8545 ATATAAACTA
* * * * *
8555 ATACTATATATGAAC--CATATA-TATGTATAAACTATATAGTTTATATATAAA--A-ATATATT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATACATAAACTATATATATA
* * * * * *
8614 ATATATAT-AACTATATA-AAAAACTATATAGTTTATA-TTATATTATTAT
66 ACATATATAAACTATGTATATAAACTATATAGATTATATTTAAATTATTAC
* * * *
8662 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATATATAAAGTGTATATATT
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATACATAAACTATATATATA
* * * *
8727 ATATATATAAACTATGTATATAAACTATATAGTTTATATTTATATTATTAT
66 ACATATATAAACTATGTATATAAACTATATAGATTATATTTAAATTATTAC
* * *
8778 ATACTATATATAAATTATATATATTATGTATAAATTATATAGTTTATTAACATAAACTATATATA
1 ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTA-T-ACATAAACTATATATA
*** *
8843 -AACA-ATATAGTTTAT-TAATATAAATTATATATGAATTATATTTAAA-TATATAC
64 TAACATATATAAACTATGT-ATATAAACTATATA-G-ATTATATTTAAATTAT-TAC
8896 AT-CT-TATAT
1 ATACTATATAT
8905 TTATATCAAC
Statistics
Matches: 207, Mismatches: 21, Indels: 21
0.83 0.08 0.08
Matches are distributed among these distances:
107 14 0.07
109 5 0.02
110 29 0.14
113 15 0.07
114 8 0.04
115 19 0.09
116 81 0.39
117 9 0.04
118 27 0.13
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (116 bp):
ATACTATATATAAACTATATATATTATGTATAAACTATATAGTGTATACATAAACTATATATATA
ACATATATAAACTATGTATATAAACTATATAGATTATATTTAAATTATTAC
Found at i:9272 original size:30 final size:31
Alignment explanation
Indices: 9229--10092 Score: 127
Period size: 28 Copynumber: 28.9 Consensus size: 31
9219 ATATAGTTTA
*
9229 AATATAAAGTATATA-A-GTACATATATAA-
1 AATATAAAGTATATATATATACATATATAAT
* *
9257 ACTATAAATTATATATATATACATATATAAT
1 AATATAAAGTATATATATATACATATATAAT
*
9288 AATATAAAGTATA-AT-TATA-A-AAACTAA-
1 AATATAAAGTATATATATATACATATA-TAAT
* *
9315 AGTATATAAGTATATA-ATATAAAGTATATAAGT
1 AATATA-AAGTATATATATATACA-TATATAA-T
*
9348 -ATATAAAGTTTTAGTACAAAGTATAAATACATATATAAT
1 AATATAAAG---TA-T----A-TATATATACATATATAAT
9387 AATATAAAGTATA-AGTATAT---TATAT-AT
1 AATATAAAGTATATA-TATATACATATATAAT
*
9414 -ATATAAAGTATA-AT-TATA-A-AGACTAA-
1 AATATAAAGTATATATATATACATATA-TAAT
* * * *
9440 AGTAT-AAGCATATA-ATATAAAGTCTATAAGT
1 AATATAAAGTATATATATATACA-TATATAA-T
*
9471 -ATAT-AA-TATA-AAATATA-AGTAT-TAA-
1 AATATAAAGTATATATATATACA-TATATAAT
*
9496 ATATA-A-AGTATATATAT----GTATATAAT
1 A-ATATAAAGTATATATATATACATATATAAT
9522 AATATAAAG--TATATATATAC--ATATAA-
1 AATATAAAGTATATATATATACATATATAAT
** *
9548 CGTAT-AAGTATGA-ATATATATATATAT-AT
1 AATATAAAGTAT-ATATATATACATATATAAT
* *
9577 -ATATATA-TATATATATATATATATATAA-
1 AATATAAAGTATATATATATACATATATAAT
* **
9605 AGT-TTTAGTATAAAGTATATATACATATATAAT
1 AATATAAAGTAT--A-TATATATACATATATAAT
*
9638 AATATAAAATTCAAGTATATATATA-AT-TATAA-
1 AATAT-AAAGT--A-TATATATATACATATATAAT
* **
9670 AGA-CTAAAGTATA-GCATATA-ATATA-AAGT
1 A-ATATAAAGTATATATATATACATATATAA-T
* * *
9699 -ATAT-AAGTATA-AAATA-AAAAATAT-AT
1 AATATAAAGTATATATATATACATATATAAT
* * *
9725 AAGTATAAA-TATAAAT-TATATATACATAAT
1 AA-TATAAAGTATATATATATACATATATAAT
* * *
9755 ATATATATA-TATATGTATATA-ATACT-T-TT
1 A-ATATAAAGTATATATATATACATA-TATAAT
** * * * *
9784 TGTAT-AAGTAT-TAAATAAAGTATATATACT
1 AATATAAAGTATATATATATA-CATATATAAT
* *
9814 -ATATATA-TATATATATATATATATAT-AT
1 AATATAAAGTATATATATATACATATATAAT
* *
9842 -ATATATA-TATATATATATATATATAT-AT
1 AATATAAAGTATATATATATACATATATAAT
* * *
9870 -ATAT-ATGTATGTATATATATATATATAAGT
1 AATATAAAGTATATATATATACATATATAA-T
* *
9900 -ATAT-ACGTATATA-ATATAAAGTATATAAGT
1 AATATAAAGTATATATATATACA-TATATAA-T
9930 ATATAATATGAAGTATATA-AGTATTA-A-ATATAAGT
1 A-AT-ATA--AAGTATATATA-TA-TACATATATAA-T
* * *
9965 -ATATAATATTAAATATAAAGTACATAAGTATATAT
1 AATATAA-AGTATATATATA-TACAT-A-TATA-AT
*
10000 AAACTATAAAGTATATATATATATATATAT-AT
1 -AA-TATAAAGTATATATATATACATATATAAT
* *
10032 ATATATATA-TATATATATATATATATATATAT
1 A-ATATAAAGTATATATATATACATATATA-AT
* *
10064 ATATATATA-TATATATATATACTTATATA
1 A-ATATAAAGTATATATATATACATATATA
10093 CTTTATTCTT
Statistics
Matches: 637, Mismatches: 81, Indels: 232
0.67 0.09 0.24
Matches are distributed among these distances:
24 6 0.01
25 19 0.03
26 28 0.04
27 77 0.12
28 135 0.21
29 65 0.10
30 87 0.14
31 46 0.07
32 64 0.10
33 12 0.02
34 9 0.01
35 25 0.04
36 16 0.03
37 16 0.03
38 8 0.01
39 2 0.00
40 17 0.03
41 5 0.01
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (31 bp):
AATATAAAGTATATATATATACATATATAAT
Found at i:9292 original size:22 final size:20
Alignment explanation
Indices: 9249--9301 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
9239 ATATAAGTAC
*
9249 ATATATAAACTATAAATTAT
1 ATATATAAACTATAAATAAT
* *
9269 ATATATATAC-ATATATAAT
1 ATATATAAACTATAAATAAT
*
9288 A-ATATAAAGTATAA
1 ATATATAAACTATAA
9302 TTATAAAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 6 0.23
19 11 0.42
20 9 0.35
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATATAAACTATAAATAAT
Found at i:9293 original size:79 final size:83
Alignment explanation
Indices: 9190--9352 Score: 185
Period size: 79 Copynumber: 2.0 Consensus size: 83
9180 AGAACCTCGA
* * *** *
9190 ATATATACTATGTATAAATTATATAGTTTATATAGTT-TAAATA-TAAAGTATATAAGTACAT-A
1 ATATATACTATATATAAATAATATAAAGTATA-A-TTATAAAAACTAAAGTATATAAGTACATAA
*
9252 TATAAACTATA-AATTATAT
64 TATAAACTATATAAGTATAT
*
9271 ATATATAC-ATATAT-AATAATATAAAGTATAATTATAAAAACTAAAGTATATAAGTATATAATA
1 ATATATACTATATATAAATAATATAAAGTATAATTATAAAAACTAAAGTATATAAGTACATAATA
*
9334 TAAAGTATATAAGTATAT
66 TAAACTATATAAGTATAT
9352 A
1 A
9353 AAGTTTTAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
77 2 0.03
78 6 0.09
79 29 0.42
80 16 0.23
81 16 0.23
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (83 bp):
ATATATACTATATATAAATAATATAAAGTATAATTATAAAAACTAAAGTATATAAGTACATAATA
TAAACTATATAAGTATAT
Found at i:9328 original size:22 final size:22
Alignment explanation
Indices: 9297--9536 Score: 120
Period size: 22 Copynumber: 11.2 Consensus size: 22
9287 TAATATAAAG
*
9297 TATAATTATA-AAAACTAAAGTA
1 TATAAGTATATAAAA-TAAAGTA
*
9319 TATAAGTATATAATATAAAGTA
1 TATAAGTATATAAAATAAAGTA
* **
9341 TATAAGTATATAAAGTTTTAGTA
1 TATAAGTATATAAA-ATAAAGTA
* *
9364 CA-AAG--TAT-AAATACA-TA
1 TATAAGTATATAAAATAAAGTA
*
9381 TATAA-TAATATAAAGTATAAGTA
1 TATAAGT-ATATAAAATA-AAGTA
* *
9404 TATTA-TATAT-ATATAAAG--
1 TATAAGTATATAAAATAAAGTA
9422 TATAA-T-TATAAAGACTAAAG--
1 TATAAGTATATAAA-A-TAAAGTA
* * *
9442 TATAAGCATATAATATAAAGTC
1 TATAAGTATATAAAATAAAGTA
*
9464 TATAAGTATATAATATAAA--A
1 TATAAGTATATAAAATAAAGTA
9484 TATAAGTAT-TAAATATAAAGTA
1 TATAAGTATATAAA-ATAAAGTA
9506 TATATATGTATATAATAATATAAAGTA
1 TATA-A-GTATAT-A-AA-ATAAAGTA
9533 TATA
1 TATA
9537 TATACATATA
Statistics
Matches: 171, Mismatches: 23, Indels: 43
0.72 0.10 0.18
Matches are distributed among these distances:
17 6 0.04
18 10 0.06
19 6 0.04
20 38 0.22
21 8 0.05
22 65 0.38
23 17 0.10
24 4 0.02
25 1 0.01
26 1 0.01
27 15 0.09
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (22 bp):
TATAAGTATATAAAATAAAGTA
Found at i:9411 original size:20 final size:20
Alignment explanation
Indices: 9388--9553 Score: 92
Period size: 20 Copynumber: 7.9 Consensus size: 20
9378 ATATATAATA
9388 ATATAAAGTATAAGTATATT
1 ATATAAAGTATAAGTATATT
*
9408 ATATATA-TATAAAGTATAATT
1 ATATAAAGTAT-AAGTAT-ATT
* *
9429 ATAAAGACTAAAGTATAAGCATATA
1 AT----A-TAAAGTATAAGTATATT
*
9454 ATATAAAGTCTATAAGTATATA
1 ATATAAAG--TATAAGTATATT
* *
9476 ATATAAAATATAAGTAT-TAA
1 ATATAAAGTATAAGTATAT-T
9496 ATATAAAGTAT-A-TATATGT
1 ATATAAAGTATAAGTATAT-T
*
9515 ATATAATAATATAAAGTATA-T
1 ATATAA-AGTAT-AAGTATATT
*
9536 ATATACA-TATAACGTATA
1 ATATAAAGTATAA-GTATA
9554 AGTATGAATA
Statistics
Matches: 118, Mismatches: 11, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
18 5 0.04
19 20 0.17
20 42 0.36
21 12 0.10
22 19 0.16
23 4 0.03
25 5 0.04
26 8 0.07
27 3 0.03
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
ATATAAAGTATAAGTATATT
Found at i:9488 original size:42 final size:42
Alignment explanation
Indices: 9408--9522 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 42
9398 TAAGTATATT
* * *
9408 ATATATATATAAAG-TATAATTATA-AAGACTAAAGTATAAGC
1 ATATA-ATATAAAGTTATAAGTATATAATACTAAAATATAAGC
*
9449 ATATAATATAAAGTCTATAAGTATATAATA-TAAAATATAAGT
1 ATATAATATAAAGT-TATAAGTATATAATACTAAAATATAAGC
9491 AT-TAAATATAAAGTATATATATGTATATAATA
1 ATAT-AATATAAAGT-TATA-A-GTATATAATA
9523 ATATAAAGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
40 8 0.13
41 6 0.10
42 35 0.56
43 4 0.06
44 10 0.16
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (42 bp):
ATATAATATAAAGTTATAAGTATATAATACTAAAATATAAGC
Found at i:9511 original size:2 final size:2
Alignment explanation
Indices: 9504--10779 Score: 370
Period size: 2 Copynumber: 645.0 Consensus size: 2
9494 AAATATAAAG
* * *
9504 TA TA TA TA TG TA TA TA -A TA -A TA TA AA GTA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
**
9545 TA -A CG TA TA -A GTA TGA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
9586 TA TA TA TA TA TA TA TA TA AA GT- TT TA GTA TA AA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA
* *
9628 CA TA TA TA -A TA -A TA TA -A AA T- TCA -A GTA TA TA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA
* * * * *
9665 TA TA AA GA CTA AA GTA TA GCA TA TA -A TA TA AA GTA TA TA -A GTA
1 TA TA TA TA -TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA
* * * * *
9708 TA -A AA TA -A AA AA TA TA TA -A GTA TA AA TA TA AA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
9747 TA CA TA -A TA TA TA TA TA TA TA TG TA TA TA -A TA CTT TT TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
9788 TA -A GTA T- TA AA TA AA GTA TA TA TA CTA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA
9829 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
* * **
9871 TA TA TG TA TG TA TA TA TA TA TA TA TA -A GTA TA TA CG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
9913 -A TA TA AA GTA TA TA -A GTA TA TA -A TA TGA -A GTA TA TA -A GTA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA T-A TA -TA TA TA TA -TA
* * * *
9953 T- TA AA TA TA -A GTA TA TA -A TA T- TA AA TA TA AA GTA CA TA -A
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
9992 GTA TA TA TA AA CTA TA AA GTA 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 TA TA TA TA TA TA
10035 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
* * * * *
10077 TA TA TA TA CT- TA TA TA CTT TA T- TC TT TA TA -A T- TA TGC TC
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A TA
*
10116 TA TA TA TA -A TA TA CT- TA TA CTT TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
10157 TA TA -A TT TA TA TA -A TA CT- TA TA TA CTT TA T- TC TT TA TA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
10196 T- TA TGC TC TA TA TA TA TA CT- TA TA CTT TA TA T- TA T- TA TA
1 TA TA T-A TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * *
10235 TG TA TA TA CTT TA TA TT TA -A TA CT- TA TA TA CTT TA TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
** * * *
10275 TA TA TA CG TG TA TA TA TA TA TA TA TA TA CT- TT TA -A T- TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * ** *
10315 T- TA T- TA TA TA TG TA TA TA TA GTT TA TA CTA AA GC TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * * *
10357 TA TA TA TA TA CA CTT TA TA GTT TA TA TA TA TA CTA TA TA CTT TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA
*
10401 TA TA TA CT- TA TA TA CT- TA TA TA T- TT TA TA T- TA TA TA CT-
1 TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
10439 TA TA TA CTT TA GTC TT TA TA -A T- TA TA -A T- TT TA TA TA TA -A
1 TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
10478 TA TA CT- TG TA CT- TA TA CTT TA TA T- TA T- TA TA TA TA CTT TA
1 TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
10518 TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TA CTA -A AA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA
* **
10558 TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TA TA CTT TA TA GG T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* *
10600 TA TA TA TA TA TA TA TA TA CT- TA TA CT- TG TA CT- TA TA TG TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA
* * *
10640 TA TA TA T- TT TA TA TA TT TA TA T- TA TA TA CT- TA TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* * * *
10681 GTC TT TA TA -A T- TA TA TA TA CA TA TA -A TA TA TT TA TA CT- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
10721 TA CTT TA TA TT TT TA TA TA TG TA TA TA TA CTT TA TA CTA -A AA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
10763 CTA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA
10780 CTTATAATGT
Statistics
Matches: 949, Mismatches: 163, Indels: 324
0.66 0.11 0.23
Matches are distributed among these distances:
1 88 0.09
2 785 0.83
3 76 0.08
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10272 original size:9 final size:8
Alignment explanation
Indices: 10079--10678 Score: 80
Period size: 7 Copynumber: 80.1 Consensus size: 8
10069 TATATATATA
10079 TATATACT
1 TATATACT
10087 TATATACT
1 TATATACT
*
10095 T-TATTCT
1 TATATACT
*
10102 T-TATA-A
1 TATATACT
*
10108 T-TATGCT
1 TATATACT
10115 CTATATA-T
1 -TATATACT
*
10123 AATATAC-
1 TATATACT
10130 T-TATACT
1 TATATACT
10137 T-TATA-T
1 TATATACT
10143 TATATA--
1 TATATACT
10149 TATATA--
1 TATATACT
*
10155 TATATAAT
1 TATATACT
10163 T-TATA--
1 TATATACT
10168 TA-ATACT
1 TATATACT
10175 TATATACT
1 TATATACT
*
10183 T-TATTCT
1 TATATACT
*
10190 T-TATA-A
1 TATATACT
*
10196 T-TATGCT
1 TATATACT
10203 CTATATA-T
1 -TATATACT
10211 ATACTTATACT
1 -TA--TATACT
10222 T-TATA-T
1 TATATACT
10228 TATTATA-T
1 TA-TATACT
10236 GTATATACT
1 -TATATACT
*
10245 T-TATATT
1 TATATACT
10252 TA-ATACT
1 TATATACT
10259 TATATACT
1 TATATACT
*
10267 T-TATATT
1 TATATACT
10274 ATATATACGT
1 -TATATAC-T
10284 GTATATA--
1 -TATATACT
10291 TATATA--
1 TATATACT
10297 TATATACT
1 TATATACT
*
10305 T-T-TAAT
1 TATATACT
*
10311 TATCTTA-T
1 TAT-ATACT
*
10319 TATATATGT
1 TATATA-CT
*
10328 ATATATAGT
1 -TATATACT
10337 T-TATAC-
1 TATATACT
10343 TA-A-AGCT
1 TATATA-CT
10350 T-TATA--
1 TATATACT
10355 TATATA-T
1 TATATACT
*
10362 ATATACACT
1 -TATATACT
*
10371 T-TATAGT
1 TATATACT
10378 T-TATA-T
1 TATATACT
10384 -ATATAC-
1 TATATACT
10390 TATATACTTT
1 TATATAC--T
10400 ATATATACT
1 -TATATACT
10409 TATATACT
1 TATATACT
10417 TATATA-T
1 TATATACT
*
10424 TTTATA-T
1 TATATACT
10431 TATATACT
1 TATATACT
10439 TATATACT
1 TATATACT
10447 T-TAGT-CT
1 TATA-TACT
*
10454 T-TATAAT
1 TATATACT
*
10461 TATA-ATTT
1 TATATA-CT
10469 TATATA-T
1 TATATACT
*
10476 AATATACTT
1 TATATAC-T
10485 GTACTTATACT
1 -TA--TATACT
10496 T-TATA-T
1 TATATACT
10502 TAT-TA--
1 TATATACT
10507 TATATACTT
1 TATATAC-T
10516 TATATTA-T
1 TATA-TACT
*
10524 TATATATGT
1 TATATA-CT
10533 ATATATACT
1 -TATATACT
10542 T-TATAC-
1 TATATACT
*
10548 TA-AAACT
1 TATATACT
10555 T-TATA-T
1 TATATACT
10561 ATATATA-T
1 -TATATACT
10569 ATATATA-T
1 -TATATACT
10577 ATATATAC-
1 -TATATACT
10585 T-TATACT
1 TATATACT
*
10592 T-TATAGGT
1 TATATA-CT
10600 TATATA--
1 TATATACT
10606 TATATA--
1 TATATACT
10612 TATATACT
1 TATATACT
10620 TATACTTGTACT
1 TATA----TACT
*
10632 TATAT-GT
1 TATATACT
*
10639 ATATATATTT
1 -TATATA-CT
10649 TATATA-T
1 TATATACT
10656 T-TATA-T
1 TATATACT
10662 TATATACT
1 TATATACT
10670 TATATACT
1 TATATACT
10678 T
1 T
10679 TAGTCTTTAT
Statistics
Matches: 463, Mismatches: 38, Indels: 182
0.68 0.06 0.27
Matches are distributed among these distances:
5 9 0.02
6 92 0.20
7 141 0.30
8 132 0.29
9 38 0.08
10 29 0.06
11 9 0.02
12 13 0.03
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (8 bp):
TATATACT
Found at i:10861 original size:2 final size:2
Alignment explanation
Indices: 10854--10886 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10844 TAACATTCAT
10854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10887 ATTGTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11214 original size:24 final size:24
Alignment explanation
Indices: 11185--11230 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
11175 TTTAGTCCAT
11185 TTTTAT-ATTAATATCAACTTCACA
1 TTTTATAATTAAT-TCAACTTCACA
*
11209 TTTTATAATTAATTCAATTTCA
1 TTTTATAATTAATTCAACTTCA
11231 TCACTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATAATTAATTCAACTTCACA
Found at i:11340 original size:3 final size:3
Alignment explanation
Indices: 11332--11360 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11322 TATAAAGTGT
11332 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
11361 AACCCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:11554 original size:20 final size:20
Alignment explanation
Indices: 11513--11561 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11503 AAATAAATAA
11513 ATTATATATACATGCATCAT
1 ATTATATATACATGCATCAT
* *
11533 ATTATCATA-ACATTCATTAT
1 ATTAT-ATATACATGCATCAT
11553 A-TATATATA
1 ATTATATATA
11562 TTATAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 15 0.60
21 3 0.12
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTATATATACATGCATCAT
Found at i:11892 original size:24 final size:24
Alignment explanation
Indices: 11847--11892 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
11837 TTCAGTCCAT
**
11847 TTTTATATTAATTTTATCTTCACA
1 TTTTATATTAATTCAATCTTCACA
11871 TTTTATAATTAATTCAAT-TTCA
1 TTTTAT-ATTAATTCAATCTTCA
11893 TCCCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATATTAATTCAATCTTCACA
Found at i:12048 original size:2 final size:2
Alignment explanation
Indices: 11967--12032 Score: 60
Period size: 2 Copynumber: 32.0 Consensus size: 2
11957 TTTGGTACTT
* * * * * *
11967 TA TA TA CA TA TA TA AA CTA TA AA GTA TA CA TG TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
12011 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
12033 AAGTATAAAG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:12107 original size:65 final size:64
Alignment explanation
Indices: 12021--12220 Score: 203
Period size: 65 Copynumber: 3.1 Consensus size: 64
12011 TATATATATA
*
12021 TATATATATATAAAGTA-TAAAGTATATAATAAAAAGTATTAAAGTATATAA-TATAAAGTAATA
1 TATATA-ATATAAAGTATTAAAGTATATAATAATAAGTATTAAA-TATA-AAGTATAAAGTAATA
12084 AG
63 AG
* * * *
12086 TGTTTGGATAT-AAGTATTAAAGTATATAA-ATATAAGTATTAAATATAAAGTATATAAGTACTA
1 TATAT-AATATAAAGTATTAAAGTATATAATA-ATAAGTATTAAATATAAAGTATA-AAGTAAT-
12149 AAG
62 AAG
* * *
12152 TATATAATATAAAGTTTTAAACTATATAAT-ATAAGTATTAAATATAAATTATTAAAGTATATAA
1 TATATAATATAAAGTATTAAAGTATATAATAATAAGTATTAAATATAAAGTA-TAAAGTA-ATAA
*
12216 A
64 G
12217 TATA
1 TATA
12221 AGTATTAAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
63 2 0.02
64 14 0.12
65 71 0.63
66 25 0.22
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (64 bp):
TATATAATATAAAGTATTAAAGTATATAATAATAAGTATTAAATATAAAGTATAAAGTAATAAG
Found at i:12210 original size:22 final size:22
Alignment explanation
Indices: 12021--12220 Score: 186
Period size: 22 Copynumber: 9.2 Consensus size: 22
12011 TATATATATA
12021 TATATATATATAAAGTA-TAAAG
1 TATATA-ATATAAAGTATTAAAG
*
12043 TATATAATAAAAAGTATTAAAG
1 TATATAATATAAAGTATTAAAG
*
12065 TATATAATATAAAGTAAT-AAG
1 TATATAATATAAAGTATTAAAG
* * *
12086 TGTTTGGATAT-AAGTATTAAAG
1 TATAT-AATATAAAGTATTAAAG
12108 TATATAA-ATATAAGTATTAAA-
1 TATATAATATA-AAGTATTAAAG
*
12129 TATA-AAGTATATAAGTACTAAAG
1 TATATAA-TATA-AAGTATTAAAG
* *
12152 TATATAATATAAAGTTTTAAAC
1 TATATAATATAAAGTATTAAAG
12174 TATATAATAT-AAGTATTAAA-
1 TATATAATATAAAGTATTAAAG
12194 TATA-AATTATTAAAGTATATAAA-
1 TATATAA-TA-TAAAGTAT-TAAAG
12217 TATA
1 TATA
12221 AGTATTAAAT
Statistics
Matches: 150, Mismatches: 15, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.01
20 10 0.07
21 36 0.24
22 84 0.56
23 16 0.11
24 2 0.01
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (22 bp):
TATATAATATAAAGTATTAAAG
Found at i:12241 original size:36 final size:35
Alignment explanation
Indices: 12131--12242 Score: 129
Period size: 36 Copynumber: 3.1 Consensus size: 35
12121 GTATTAAATA
*
12131 TAAAGTATATAAGTACTAAAGTATATAATATAAAGTT-T
1 TAAAGTATATAAATA-T-AAGTAT-TAA-ATAAAGTTAT
* *
12169 TAAACTATAT-AATATAAGTATTAAATATAAATTAT
1 TAAAGTATATAAATATAAGTATTAAATA-AAGTTAT
12204 TAAAGTATATAAATATAAGTATTAAATAAAGTATAT
1 TAAAGTATATAAATATAAGTATTAAATAAAGT-TAT
12240 TAA
1 TAA
12243 TTATCATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
33 3 0.05
34 7 0.11
35 19 0.29
36 24 0.37
37 3 0.05
38 9 0.14
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (35 bp):
TAAAGTATATAAATATAAGTATTAAATAAAGTTAT
Found at i:12257 original size:26 final size:26
Alignment explanation
Indices: 12103--12257 Score: 75
Period size: 26 Copynumber: 6.1 Consensus size: 26
12093 ATATAAGTAT
12103 TAAAGTATATAAATATAAGT-ATTAAATA
1 TAAAGTATATAAATATAAGTAATT--A-A
* *
12131 TAAAGTATATAAGTACTAAAGTATATAATA
1 TAAAGTATATAAATA-T-AAGTA-ATTA-A
*
12161 TAAAGT-TTTAAACTAT-A-TAA-T-A
1 TAAAGTATATAAA-TATAAGTAATTAA
*
12183 T-AAGTAT-TAAATAT-A--AATTAT
1 TAAAGTATATAAATATAAGTAATTAA
12204 TAAAGTATATAAATATAAGT-ATTAAA
1 TAAAGTATATAAATATAAGTAATT-AA
* *
12230 TAAAGTATATTAATTATCA-TAATTAA
1 TAAAGTATA-TAAATATAAGTAATTAA
12256 TA
1 TA
12258 TATTAAGTAT
Statistics
Matches: 102, Mismatches: 9, Indels: 34
0.70 0.06 0.23
Matches are distributed among these distances:
19 2 0.02
20 5 0.05
21 9 0.09
22 9 0.09
23 7 0.07
24 1 0.01
25 4 0.04
26 17 0.17
27 11 0.11
28 14 0.14
29 6 0.06
30 15 0.15
32 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (26 bp):
TAAAGTATATAAATATAAGTAATTAA
Found at i:12442 original size:16 final size:16
Alignment explanation
Indices: 12394--12449 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
12384 TTTCATCAAT
*
12394 GGTAATATATAAG-TCA
1 GGTAA-ATATCAGATCA
*
12410 GGTAAATGTCA-AGTCA
1 GGTAAATATCAGA-TCA
12426 GGTAAATATCAGATCA
1 GGTAAATATCAGATCA
*
12442 GGTCAATA
1 GGTAAATA
12450 ACAAGTCGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 28 0.85
17 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (16 bp):
GGTAAATATCAGATCA
Found at i:12485 original size:32 final size:32
Alignment explanation
Indices: 12449--12522 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
12439 TCAGGTCAAT
*
12449 AACAAGTCGGA-TCATTTACA-GACCAGGTTGAA
1 AACAAGTCGGATTCA-TAACATG-CCAGGTTGAA
* *
12481 AACAAGTCAGATTCATAACATGTCAGGTTGAA
1 AACAAGTCGGATTCATAACATGCCAGGTTGAA
*
12513 AACAGGTCGG
1 AACAAGTCGG
12523 GTAATACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (32 bp):
AACAAGTCGGATTCATAACATGCCAGGTTGAA
Found at i:12516 original size:16 final size:16
Alignment explanation
Indices: 12472--12516 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
12462 ATTTACAGAC
12472 CAGGTTGAAAACAAGT
1 CAGGTTGAAAACAAGT
* * * *
12488 CAGATTCATAACATGT
1 CAGGTTGAAAACAAGT
12504 CAGGTTGAAAACA
1 CAGGTTGAAAACA
12517 GGTCGGGTAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (16 bp):
CAGGTTGAAAACAAGT
Found at i:23955 original size:13 final size:13
Alignment explanation
Indices: 23937--23961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23927 CGAACCGGTC
23937 TGACCCGACCCGT
1 TGACCCGACCCGT
23950 TGACCCGACCCG
1 TGACCCGACCCG
23962 ACCCATTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:23961 original size:18 final size:18
Alignment explanation
Indices: 23938--23977 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
23928 GAACCGGTCT
*
23938 GACCCGACCCGTTGACCC
1 GACCCGACCCATTGACCC
23956 GACCCGACCCATTGACCC
1 GACCCGACCCATTGACCC
23974 GACC
1 GACC
23978 TGTGAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.10
Consensus pattern (18 bp):
GACCCGACCCATTGACCC
Found at i:28257 original size:63 final size:63
Alignment explanation
Indices: 28156--28475 Score: 523
Period size: 63 Copynumber: 5.1 Consensus size: 63
28146 ATGCATGTTG
* *
28156 TATTATTTATACATATATTTAACAGATTTTCTAATTGGATTCGGATTTCTTTTAATATGATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTCGGATTTCTTTTAATATTATTT
*
28219 TATTATTTATACATATATTTAATAGATTTTCTATTTGGATTCGGATTTCTTTTAATATTATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTCGGATTTCTTTTAATATTATTT
* * * *
28282 TATTATTCATACATATATTTAATAGTTTTTCTATTTGGATTCGGATTTCTTTTAATATGATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTCGGATTTCTTTTAATATTATTT
* * *
28345 TATTATTTATACATATATTTAATAGTTTTTCTAATTGGATTTGGATTTCATTTAATATTATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTCGGATTTCTTTTAATATTATTT
* * *
28408 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTTGGGTTTCATTTAATATTATTT
1 TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTCGGATTTCTTTTAATATTATTT
28471 TATTA
1 TATTA
28476 AATCCTAGTC
Statistics
Matches: 244, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 244 1.00
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (63 bp):
TATTATTTATACATATATTTAATAGATTTTCTAATTGGATTCGGATTTCTTTTAATATTATTT
Found at i:29208 original size:54 final size:54
Alignment explanation
Indices: 29121--29224 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
29111 AAAGTAATCA
* * *
29121 TTAATCCATAAATGAATGTTTCAAGCTTATGGTATTCTATATATGTATATTACT
1 TTAAGCCATAAATGAATGTTTCAAGCGTATGGTATTCTATATATATATATTACT
*
29175 TTAAGCCATAAATGAATGTTTCAGGCGTATGGTATTCTATATATATATAT
1 TTAAGCCATAAATGAATGTTTCAAGCGTATGGTATTCTATATATATATAT
29225 ATATATATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (54 bp):
TTAAGCCATAAATGAATGTTTCAAGCGTATGGTATTCTATATATATATATTACT
Found at i:35401 original size:48 final size:48
Alignment explanation
Indices: 35326--35428 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
35316 CTGGATTTGA
35326 TGAA-ATAGGATGAATTGAGACGGTATTTTGTAAATACGTAATTATAT
1 TGAATATAGGATGAATTGAGACGGTATTTTGTAAATACGTAATTATAT
35373 TGAATATAGGATGAATTGAGACGGTATTTTGTAAATACGTAATTATAT
1 TGAATATAGGATGAATTGAGACGGTATTTTGTAAATACGTAATTATAT
35421 TGAATATA
1 TGAATATA
35429 TTAATTATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 4 0.07
48 51 0.93
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (48 bp):
TGAATATAGGATGAATTGAGACGGTATTTTGTAAATACGTAATTATAT
Found at i:43465 original size:15 final size:13
Alignment explanation
Indices: 43437--43462 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43427 AAAGTTTGAT
43437 TGATTTTTTTAAA
1 TGATTTTTTTAAA
43450 TGATTTTTTTAAA
1 TGATTTTTTTAAA
43463 AATAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TGATTTTTTTAAA
Found at i:45918 original size:45 final size:46
Alignment explanation
Indices: 45830--45920 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
45820 TTGAAAAAGC
* *
45830 CTGAGTGCATCGATGCATAGTCTTATGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATATGCATCGATGCATAAAATGCA
* *
45876 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATATGCATCGATGCATAAAATGCA
45921 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATATGCATCGATGCATAAAATGCA
Found at i:48669 original size:44 final size:44
Alignment explanation
Indices: 48580--48676 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
48570 GCTCTTGTGC
* *
48580 ATCGATGCACATTCAAGGGCGTGCATCAGTGCATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCAGTGCATCAGCTAATGT
* * *
48624 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCAGTGCATCAGCTAA-TGT
48668 ATCGATGCA
1 ATCGATGCA
48677 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCAGTGCATCAGCTAATGT
Found at i:52050 original size:16 final size:16
Alignment explanation
Indices: 52029--52081 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
52019 ATTTCTAATT
52029 TTTGGTACCCAAATCC
1 TTTGGTACCCAAATCC
*
52045 TTTGGTACCCAGATCC
1 TTTGGTACCCAAATCC
*
52061 TTTGGTACCCAAACCC
1 TTTGGTACCCAAATCC
52077 TTTGG
1 TTTGG
52082 GTCCATATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (16 bp):
TTTGGTACCCAAATCC
Found at i:55096 original size:43 final size:43
Alignment explanation
Indices: 55036--55122 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
55026 TTTGAAAAGC
* * *
55036 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATG-ATCAAATG
1 CTGAGTGAATCGATGCATAGT-ATGTGCATCGATGCATAAAATG
*
55079 CTGAGTGAATCGATGCATGGTATGTGCATCGATGCATAAAATG
1 CTGAGTGAATCGATGCATAGTATGTGCATCGATGCATAAAATG
55122 C
1 C
55123 ATTCGATGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 12 0.31
43 27 0.69
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
CTGAGTGAATCGATGCATAGTATGTGCATCGATGCATAAAATG
Done.